[gmx-users] REMD
Hello Gromacs Users, I am interested in calculating the equilibrium distribution of molecular structures at the vacuum-liquid interface of several different low vapor pressure liquids. All of these liquids are very viscous at or near room-temperature and I suspect that conformational barriers may inhibit sampling at the vacuum-liquid interface. However, in NVT MD simulations, these liquids increase fluidity at higher temperatures (400-500K) while maintaining a fluid state and a reasonably well-defined vacuum-liquid interface. Can I use NVT REMD to efficiently overcome any kinetic trapping that might be going on and obtain a true equilibrium distribution of molecular structures at the vacuum-liquid interface? A superficial literature search does not yield examples of NVT REMD on a liquid interface. I am curious if there are issues or complications with this approach. Is there a better alternative? the manual states that "all possible pairs are tested for exchange" in Gibbs REMD. Looking through the mdrun help output, it seems like this option can be selected by setting the "-nex" flag. However, the comment for this flag suggests using N^3. Isn't something like N*(N-1)/2 more appropriate (where N is the number of replicas). Thanks for the guidance! Best, Eric -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD
Hello GROMACS users, As far as I understand, increasing the number of random exchanges to a large number (mdrun suggests N^3 where N is the number of replicas) moves a REMD simulation from a neighbor exchange procedure to a Gibbs exchange procedure. Can anyone provide some practical advice or references useful in deciding which to use? Naively, I would guess that a Gibbs exchange procedure would converge faster for a REMD equilibration with a large number of replicas (~100). Is this usually true? Best, Eric -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD
Hi, I have some doubt regarding REMD simulation. 1. In the .mdp file of each replica is it necessary to keep the gen-temp constant? as example: 300 k is the lowest temp of REMD simulation. Is it necessary to keep the gen-temp=300 in each replica. 2. Is it necessary to provide -replex flag during the equilbration phase of REMD simulation -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD
Hello gmx users, I am getting an error "load imbalance " in remd nvt equilibrium step. Can anyone help me regarding this issue? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD
Sir, I want to do an REMD simulation having 16 replicas. But I have only 8 processors. Is it possible to do 16 replicas in 8 processors? How I can do this? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD error
Hi,
I am running a REMD of a protein, when I submit "gmx mdrun -s md_0_${i}.tpr
-multi 46 -replex 1000 -reseed -1", it fails as the below
Fatal error:
mdrun -multi or -multidir are not supported with the thread-MPI library. Please
compile GROMACS with a proper external MPI library.
I have installed the openmpi and gromacs 5.1.
Do anyone know the problem.
yours sincerelly,
Ouyang
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[gmx-users] REMD analysis
Dear all, I have performed an REMD simulation for protein drug system (8350 + 32500 sol) using gromacs-4.4.5 package. But I could not understand how to do analysis of REMD. I have used 10 set of replicas (298 K to 308.31K with r=1.0038, the common ratio of the geometric progression) for REMD simulation and carried out a 5 ns simulation. I would like to compare the thermodynamics of two drug molecules using REMD. Can you please suggest me, how can I plot potential energy vs probability or how can I get free energy profile? What types of analysis do I need to understand REMD? Looking forward to hear from you. Thanks in advance, Kalyanashis Jana -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD Simulation
Dear all, I am trying to do REMD simulation in different cosolvents. I have generated temperatures using temperature genrating tools but it gives different number of temperatures in different solvents with exchange probability of 0.25. Is it fair to do remd with different replicas? In what way it will effect the results? Thankyou -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD temperature_space
Dear gromacs users, can anyone please suggest me that how we get the time evolution of a replica (say replica_1) in temperature space and time courses of potential energy of each replica( one way is md.edr file??) As according to GROMACS tutorial, I used demux.pl script and got two files replica_index.xvg and replica_temp.xvg. But I want to analyse a single replica trajectory in all temperatures ( temp. on y-axis) Thank you in advance.. Sundari -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD tutorial
Dear Mark Before, in following address you said: Google knows about two GROMACS REMD tutorials. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-January/086563.html Unfortunately, I could not find tutorials you mentioned. Also, in following address you said: I've added a section on replica-exchange to http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2007-December/031188.html . Is this link active, now? I have no access to this link. - I want to know Is there a tutorial for REMD like what is in http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/. Any help will highly appreciated. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD Plots
Dear Gromacs users, How do we plot a graph for temperature vs swap step number using a REMD simulation with 30 systems. I already generated the replica_temp.xvg and replica_index.xvg files using demux.pl script. Thank you. Best Regards Shan Jayasinghe -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] remd error
Hi,
I am running remd simulation in gromacs-2016.5. After generating the
multiple .tpr file in each directory by the following command
*for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro -p
topol.top -o remd$i.tpr -maxwarn 1; cd ..; done*
I run *mpirun -np 80 gmx_mpi mdrun -s remd.tpr -multi 8 -replex 1000
-reseed 175320 -deffnm remd_equil*
It is giving the following error
There are not enough slots available in the system to satisfy the 40 slots
that were requested by the application:
gmx_mpi
Either request fewer slots for your application, or make more slots
available
for use.
--
--
There are not enough slots available in the system to satisfy the 40 slots
that were requested by the application:
gmx_mpi
Either request fewer slots for your application, or make more slots
available
for use.
--
I am not understanding the error. Any suggestion will be highly
appriciated. The mdp file and the qsub.sh file is attached below
qsub.sh...
#! /bin/bash
#PBS -V
#PBS -l nodes=2:ppn=20
#PBS -l walltime=48:00:00
#PBS -N mdrun-serial
#PBS -j oe
#PBS -o output.log
#PBS -e error.log
#cd /home/bratin/Downloads/GROMACS/Gromacs_fibril
cd $PBS_O_WORKDIR
module load openmpi3.0.0
module load gromacs-2016.5
NP='cat $PBS_NODEFILE | wc -1'
# mpirun --machinefile $PBS_PBS_NODEFILE -np $NP 'which gmx_mpi' mdrun -v
-s nvt.tpr -deffnm nvt
#/apps/gromacs-2016.5/bin/mpirun -np 8 gmx_mpi mdrun -v -s remd.tpr -multi
8 -replex 1000 -deffnm remd_out
for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro -r
em.gro -p topol.top -o remd$i.tpr -maxwarn 1; cd ..; done
for i in {0..7}; do cd equil${i}; mpirun -np 40 gmx_mpi mdrun -v -s
remd.tpr -multi 8 -replex 1000 -deffnm remd$i_out ; cd ..; done
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Re: [gmx-users] REMD
On 7/31/19 1:44 AM, Bratin Kumar Das wrote: Hi, I have some doubt regarding REMD simulation. 1. In the .mdp file of each replica is it necessary to keep the gen-temp constant? as example: 300 k is the lowest temp of REMD simulation. Is it necessary to keep the gen-temp=300 in each replica. No, because each subsystem needs to be equilibrated independently at the desired temperature. 2. Is it necessary to provide -replex flag during the equilbration phase of REMD simulation No, because these simulations are independent of one another. Only during the actual REMD do you need -replex. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD
Thanks for clarification. On Thu, Aug 1, 2019 at 7:43 PM Justin Lemkul wrote: > > > On 7/31/19 1:44 AM, Bratin Kumar Das wrote: > > Hi, > > I have some doubt regarding REMD simulation. > > 1. In the .mdp file of each replica is it necessary to keep the > > gen-temp constant? > > as example: 300 k is the lowest temp of REMD simulation. Is it necessary > to > > keep the gen-temp=300 in each replica. > > No, because each subsystem needs to be equilibrated independently at the > desired temperature. > > > 2. Is it necessary to provide -replex flag during the equilbration > > phase of REMD simulation > > No, because these simulations are independent of one another. Only > during the actual REMD do you need -replex. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD-error
Dear all, I am running one REMD simulation with 65 replicas. I am using 130 cores for the simulation. I am getting the following error. Fatal error: Your choice of number of MPI ranks and amount of resources results in using 16 OpenMP threads per rank, which is most likely inefficient. The optimum is usually between 1 and 6 threads per rank. If you want to run with this setup, specify the -ntomp option. But we suggest to change the number of MPI ranks. when I am using -ntomp option ...it is throwing another error Fatal error: Setting the number of thread-MPI ranks is only supported with thread-MPI and GROMACS was compiled without thread-MPI while GROMACS is compiled with threated-MPI... plerase help me in this regard. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] remd
On 11/14/13 1:05 AM, Shine A wrote: sir, I have a basic doubt about remd simulation. In remd is it possible to run 16 replicas in 8 processors? No. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gromacs.org_gmx-users mailing listgromacs.org_gmx-users@maillist.sys.kth.se https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] remd
Yes, just tell your MPI setup to do that. Performance will degrade, and mdrun will complain that it can't set processor affinities, which is fine for your purpose. Mark On Nov 14, 2013 7:06 AM, "Shine A" wrote: > sir, > > I have a basic doubt about remd simulation. In remd is it possible to > run 16 replicas in 8 processors? > -- > gmx-users mailing listgmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gromacs.org_gmx-users mailing listgromacs.org_gmx-users@maillist.sys.kth.se https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] REMD exchange probabilities
Dear list, Using an exchange probability of 0.25 and temperature range 293-370 K, I calculated number of replicas using the server. However, when I did first run and tried exchanging replicas every 500 steps (1 ps), I don't think the exchange probabilities make sense in particular replicas 15 and 16. Replica 15 has a low exchange ratio of 0.12 while replica 16 has a high exchange ratio of 0.55. Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 Repl .28 .28 .28 .28 .29 .28 .29 .29 .28 .29 .28 .28 .29 .29 .29 .12 .55 .29 .29 .30 .30 .29 .29 .26 .32 .31 .30 .30 .30 .30 .30 .31 .31 .31 .31 .31 .31 .31 .31 .31 .31 .31 .32 .32 .32 .32 .33 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 Repl 2901 2954 2873 3017 3038 2910 3009 2993 2934 3002 2981 2999 2927 3038 3059 1229 5757 3056 3100 3136 3054 3053 3109 2743 3166 3097 3185 3161 3189 3133 3226 3261 3242 3229 3205 3249 3227 3221 3222 3326 3303 3309 3320 3373 3346 3474 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 Repl .28 .28 .27 .29 .29 .28 .29 .29 .28 .29 .29 .29 .28 .29 .29 .12 .55 .29 .30 .30 .29 .29 .30 .26 .32 .30 .30 .30 .30 .31 .30 .31 .31 .31 .31 .31 .31 .31 .31 .31 .32 .32 .32 .32 .32 .32 .33 Below are the temperatures I have used. How do I manually edit temperatures to get average exchange probabilities between 0.2-0.3? ref_t= 293293; reference temperature, one for each group, in K ref_t= 294.51 294.51; reference temperature, one for each group, in K ref_t= 296.03 296.03; reference temperature, one for each group, in K ref_t= 297.56 297.56; reference temperature, one for each group, in K ref_t= 299.09 299.09; reference temperature, one for each group, in K ref_t= 300.63 300.63; reference temperature, one for each group, in K ref_t= 302.18 302.18; reference temperature, one for each group, in K ref_t= 303.73 303.73; reference temperature, one for each group, in K ref_t= 305.29 305.29; reference temperature, one for each group, in K ref_t= 306.86 306.86; reference temperature, one for each group, in K ref_t= 308.43 308.43; reference temperature, one for each group, in K ref_t= 310.01 310.01; reference temperature, one for each group, in K ref_t= 311.60 311.60; reference temperature, one for each group, in K ref_t= 313.19 313.19; reference temperature, one for each group, in K ref_t= 314.79 314.79; reference temperature, one for each group, in K ref_t= 316.40 316.40; reference temperature, one for each group, in K ref_t= 318.63 318.63; reference temperature, one for each group, in K ref_t= 319.63 319.63; reference temperature, one for each group, in K ref_t= 321.26 321.26; reference temperature, one for each group, in K ref_t= 322.89 322.89; reference temperature, one for each group, in K ref_t= 324.52 324.52; reference temperature, one for each group, in K ref_t= 326.17 326.17; reference temperature, one for each group, in K ref_t= 327.82 327.82; reference temperature, one for each group, in K ref_t= 329.49 329.49; reference temperature, one for each group, in K ref_t= 331.26 331.26; reference temperature, one for each group, in K ref_t= 332.86 332.86; reference temperature, one for each group, in K ref_t= 334.51 334.51; reference temperature, one for each group, in K ref_t= 336.20 336.20; reference temperature, one for each group, in K ref_t= 337.90 337.90; reference temperature, one for each group, in K ref_t= 339.61 339.61; reference temperature, one for each group, in K ref_t= 341.32 341.32; reference temperature, one for each group, in K ref_t= 343.04 343.04; reference temperature, one for each group, in K ref_t= 344.76 344.76; reference temperature, one for each group, in K ref_t= 346.49 346.49; reference temperature, one for each group, in K re
[gmx-users] REMD mdrun_mpi error
Dear gromacs users, I am trying to simulate a ligand using REMD method in explicit solvent with the charmm force field. When I try to equilibrate my system I get this error : Double sids (0, 1) for atom 26 Double sids (0, 1) for atom 27 Double sids (0, 1) for atom 28 Double sids (0, 1) for atom 29 Double sids (0, 1) for atom 30 Double sids (0, 1) for atom 31 Double sids (0, 1) for atom 32 Double sids (0, 1) for atom 33 Double sids (0, 1) for atom 34 Double sids (0, 1) for atom 35 Double sids (0, 1) for atom 36 Double sids (0, 1) for atom 37 Double sids (0, 1) for atom 38 Double sids (0, 1) for atom 39 Double sids (0, 1) for atom 40 --- Program mdrun_mpi, VERSION 4.6.5 Source code file: /local/software/gromacs/4.6.5/source/gromacs-4.6.5/src/gmxlib/invblock.c, line: 99 Fatal error: Double entries in block structure. Item 53 is in blocks 1 and 0 Cannot make an unambiguous inverse block. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors *My mdp input file looks like this :* *title = CHARMM compound NVT equilibration define = -DPOSRES ; position restrain the protein; Run parametersintegrator = sd; leap-frog stochastic dynamics integratornsteps = 100 ; 2 * 100 = 100 psdt = 0.002 ; 2 fs; Output controlnstxout = 500 ; save coordinates every 0.2 psnstvout = 10; save velocities every 0.2 psnstenergy = 500 ; save energies every 0.2 psnstlog = 500 ; update log file every 0.2 ps; Bond parameterscontinuation= no; first dynamics runconstraint_algorithm = SHAKE; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrainedshake-tol = 0.1 ; relative tolerance for SHAKE; Neighborsearchingns_type = grid ; search neighboring grid cellsnstlist = 5 ; 10 fsrlist = 1.0 ; short-range neighborlist cutoff (in nm)rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm)rvdw= 1.0 ; short-range van der Waals cutoff (in nm); Electrostaticscoulombtype = PME ; Particle Mesh Ewald for long-range electrostaticspme_order = 4 ; Interpolation order for PME. 4 equals cubic interpolationfourierspacing = 0.16 ; grid spacing for FFT; Temperature coupling is on;tcoupl = V-rescale ; modified Berendsen thermostattc-grps = LIG SOL ; two coupling groups - more accuratetau_t = 1.0 1.0 ; time constant, in psref_t = X X ; reference temperature, one for each group, in K;Langevin dynamicsbd-fric = 0 ; ;Brownian dynamics friction coefficient. ld-seed =-1;;pseudo random seed is used; Pressure coupling is offpcoupl = no; no pressure coupling in NVT; Periodic boundary conditionspbc = xyz ; 3-D PBC; Dispersion correctionDispCorr= EnerPres ; account for cut-off vdW scheme; Velocity generationgen_vel = yes ; assign velocities from Maxwell distributiongen_temp= 0.0 ; temperature for Maxwell distributiongen_seed= -1; generate a random seed* *And my input file to run it in parallel looks like that:* *#!/bin/bash#PBS -l nodes=3:ppn=16#PBS -l walltime=00:10:00#PBS -o zzz.qsub.out#PBS -e zzz.qsub.errmodule load openmpi module load gromacs/4.6.5mpirun -np 48 mdrun_mpi -s eq_.tpr -multi 48 -replex 10 >& faillog-X.log* Does anyone have seen this issue before?? Many thanks, -- Nawel Mele, PhD Research Student Jonathan Essex Group, School of Chemistry University of Southampton, Highfield Southampton, SO17 1BJ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD temperature trajectory
Dear Gromacs user, I performed a REMD simulation and I want to analyse my result per temperature. I am interested at looking the trajectory for the lowest and the highest temperature. I am used to perform REMD with Amber and I realised that Amber exchanges temperature during the simulation,compare to Gromacs which returns a discontinuous trajectories for each temperatures. So my question is , do I need to use the demux.pl script to get a "temperature trajectory" or can I, from the log output file, just create a trajectory at the temperature of interest? For example if I am interested on the lowest temperature, should I just need to analyse the prod0.log file?? Another question, the output replica_temp.xvg from the demux.pl looks like this : 0 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 2 1023546789 10 11 13 12 14 15 16 17 18 19 21 20 23 22 24 25 27 26 28 29 31 30 33 32 34 35 37 36 39 38 41 40 43 42 44 45 46 47 4 201364587 10 9 11 13 12 14 15 16 17 18 20 22 19 24 21 23 26 28 25 27 30 32 29 33 31 34 35 37 36 40 38 41 39 44 42 43 46 45 47 6 310264597 11 8 10 12 13 15 14 16 17 19 20 22 18 24 21 23 27 29 25 26 30 32 28 33 31 34 35 37 36 41 39 40 38 45 43 42 47 44 46 Does that mean that, except for the first column, each column corresponds to each temperature? An so from that we can follow the trajectory of the replicas for a temperature of interest? Many thanks in advance Nawel -- Nawel Mele, PhD Research Student Jonathan Essex Group, School of Chemistry University of Southampton, Highfield Southampton, SO17 1BJ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD of IDPs
Hi, I have a sequence of an intrinsically disordered protein, I have no idea how to start my REMD with gromacs. e.g. how to convert my sequence into a pdb file -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD error
Hi,
Yes. Exactly as the error message says, you need to compile GROMACS
differently, with real MPI support. See
http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-features.html#running-multi-simulations
Mark
On Fri, May 13, 2016 at 9:47 AM YanhuaOuyang <15901283...@163.com> wrote:
> Hi,
> I am running a REMD of a protein, when I submit "gmx mdrun -s
> md_0_${i}.tpr -multi 46 -replex 1000 -reseed -1", it fails as the below
> Fatal error:
> mdrun -multi or -multidir are not supported with the thread-MPI library.
> Please compile GROMACS with a proper external MPI library.
> I have installed the openmpi and gromacs 5.1.
> Do anyone know the problem.
>
> yours sincerelly,
> Ouyang
> --
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Re: [gmx-users] REMD error
Hi,
I have installed the openmpi 1.10, and I can run mpirun. When I installed
grimaces 5.1, I configured -DGMX_MPI=on.
And the error still happens .
> 在 2016年5月13日，下午3:59，Mark Abraham 写道：
>
> Hi,
>
> Yes. Exactly as the error message says, you need to compile GROMACS
> differently, with real MPI support. See
> http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-features.html#running-multi-simulations
>
> Mark
>
> On Fri, May 13, 2016 at 9:47 AM YanhuaOuyang <15901283...@163.com> wrote:
>
>> Hi,
>> I am running a REMD of a protein, when I submit "gmx mdrun -s
>> md_0_${i}.tpr -multi 46 -replex 1000 -reseed -1", it fails as the below
>> Fatal error:
>> mdrun -multi or -multidir are not supported with the thread-MPI library.
>> Please compile GROMACS with a proper external MPI library.
>> I have installed the openmpi and gromacs 5.1.
>> Do anyone know the problem.
>>
>> yours sincerelly,
>> Ouyang
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
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>>
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
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Re: [gmx-users] REMD error
Hi,
If you've configured with GMX_MPI, then the resulting GROMACS binary is
called gmx_mpi, so mpirun -np X gmx_mpi mdrun -multi ...
Mark
On Fri, May 13, 2016 at 10:09 AM YanhuaOuyang <15901283...@163.com> wrote:
> Hi,
> I have installed the openmpi 1.10, and I can run mpirun. When I installed
> grimaces 5.1, I configured -DGMX_MPI=on.
> And the error still happens .
> > 在 2016年5月13日，下午3:59，Mark Abraham 写道：
> >
> > Hi,
> >
> > Yes. Exactly as the error message says, you need to compile GROMACS
> > differently, with real MPI support. See
> >
> http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-features.html#running-multi-simulations
> >
> > Mark
> >
> > On Fri, May 13, 2016 at 9:47 AM YanhuaOuyang <15901283...@163.com>
> wrote:
> >
> >> Hi,
> >> I am running a REMD of a protein, when I submit "gmx mdrun -s
> >> md_0_${i}.tpr -multi 46 -replex 1000 -reseed -1", it fails as the below
> >> Fatal error:
> >> mdrun -multi or -multidir are not supported with the thread-MPI library.
> >> Please compile GROMACS with a proper external MPI library.
> >> I have installed the openmpi and gromacs 5.1.
> >> Do anyone know the problem.
> >>
> >> yours sincerelly,
> >> Ouyang
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
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> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> > --
> > Gromacs Users mailing list
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> posting!
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[gmx-users] REMD implicit solvent
Dear gromacs users, I am trying to run REMD simulations using 4.5.5 version (implicit solvent). The MD procedure: pdb2gmx -f prot.pdb -o prot.gro -q prot.pdb -ignh -ss. The input for minimization step: ; Run control parameters integrator = cg nsteps = 800 vdwtype = cut-off coulombtype = cut-off ;cutoff-scheme= group pbc = no periodic_molecules = no nstlist = 10 ns_type = grid rlist= 1.0 rcoulomb = 1.6 rvdw = 1.6 comm-mode= Angular nstcomm = 10 ; ;Energy minimizing stuff ; emtol= 100.0 nstcgsteep = 2 emstep = 0.01 ; ;Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; ; Implicit solvent ; implicit_solvent = GBSA gb_algorithm = OBC ;Still HCT OBC nstgbradii = 1.0 rgbradii = 1.0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent gb_saltconc = 0; Salt concentration for implicit solvent models, currently not used sa_algorithm = Ace-approximation sa_surface_tension = 2.05016 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA. The value -1 will set default value for Still/HCT/OBC GB-models. and it finished without errors. The problem is with equilibration step. The input file that I used is: ; MD CONTROL OPTIONS integrator = md dt = 0.002 nsteps = 5 ; 10 ns init_step = 0; For exact run continuation or redoing part of a run comm-mode = Angular ; mode for center of mass motion removal nstcomm = 10 ; number of steps for center of mass motion removal ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency for energies to log file and energy file nstlog = 1000 nstcalcenergy= 10 nstenergy= 1000 ; Neighbor searching and Electrostatitcs vdwtype = cut-off coulombtype = cut-off ;cutoff-scheme= group pbc = no periodic_molecules = no nstlist = 5 ns_type = grid rlist= 1.0 rcoulomb = 1.6 rvdw = 1.0 ; Selection of energy groups energygrps = fixed not_fixed freezegrps = fixed not_fixed freezedim= Y Y Y N N N ;Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Temperutare coupling tcoupl = v-rescale tc_grps = fixed not_fixed tau_t= 0.01 0.01 ;nst_couple = 5 ref_t= 300.00 300.00 ; Pressure coupling pcoupl = no ;pcoupletype = isotropic tau_p= 1.0 ;compressiblity = 4.5e-5 ref_p= 1.0 gen_vel = yes gen_temp = 300.00 300.00 gen_seed = -1 constraints = h-bonds ; Implicit solvent implicit_solvent = GBSA gb_algorithm = Still ; HCT ; OBC nstgbradii = 1.0 rgbradii = 1.0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent gb_saltconc = 0; Salt concentration for implicit solvent models, currently not used sa_algorithm = Ace-approximation sa_surface_tension = 2.05016 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA. The value -1 will set default value for Still/HCT/OBC GB-models. mdrun -v -multidir eq_[12345678] The error that I obtained is: Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I do not know what is wrong. I checked the Fatal error at www.gromacs.org/Documentation/Errors. My system is ok, I tried to increase the min steps but did not help. I have also checked the http://www.gromacs.org/Documentation/How-tos/REMD but can not move forward because of equilibration step. I appreciate any recommendation. Thanks Urszula Urszula Uciechowska PhD University of Gdansk and Medical Univesity of Gdansk Dep
[gmx-users] REMD DLB bug
Hello All, I was running REMD simulations on Gromacs 2016.1 when my simulation crashed with the error Assertion failed: Condition: comm->cycl_n[ddCyclStep] > 0 When we turned on DLB, we should have measured cycles I saw that there was a bug #2298 reported about this recently at https://redmine.gromacs.org/issues/2298. I wanted to know if this fix has been implemented in the latest 2018 or 2016.4 versions? Thanks, Akshay -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD Simulation
Hi, On Mon, Apr 16, 2018 at 10:21 AM ISHRAT JAHAN wrote: > Dear all, > I am trying to do REMD simulation in different cosolvents. I have generated > temperatures using temperature genrating tools but it gives different > number of temperatures in different solvents with exchange probability of > 0.25. Is it fair to do remd with different replicas? Sure. But first you should understand why the number of degrees of freedom in the system are relevant for affecting the temperature spacing required for constant exchange probability. See, among other references https://pubs.acs.org/doi/abs/10.1021/ct800016r (shameless self-plug...) > In what way it will > effect the results? > What results are you seeking? Why would the number of replicas be a relevant parameter determining the result? Mark > Thankyou > -- > Ishrat Jahan > Research Scholar > Department Of Chemistry > A.M.U Aligarh > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD temperature_space
Hi, It sounds like you just want to use the original data, which you had before you ran the demux script. Mark On Thu, May 3, 2018 at 1:28 PM Sundari wrote: > Dear gromacs users, > > can anyone please suggest me that how we get the time evolution of a > replica (say replica_1) in temperature space and time courses of potential > energy of each replica( one way is md.edr file??) > As according to GROMACS tutorial, I used demux.pl script and got two files > replica_index.xvg and replica_temp.xvg. But I want to analyse a single > replica trajectory in all temperatures ( temp. on y-axis) > > > Thank you in advance.. > > Sundari > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD temperature_space
Hello, I got the continuous trajectories by using demux. But now I am confused in getting potential energy distribution of a single replica (similarly time evolution of a replica (say replica_1) in temperature space). I used edr file of original production data files, but I am not getting what I want. I am attaching the temp.xvg file of one replica (say T= 315K replica) Thank You.. On Thu, May 3, 2018 at 5:02 PM, Mark Abraham wrote: > Hi, > > It sounds like you just want to use the original data, which you had before > you ran the demux script. > > Mark > > On Thu, May 3, 2018 at 1:28 PM Sundari wrote: > > > Dear gromacs users, > > > > can anyone please suggest me that how we get the time evolution of a > > replica (say replica_1) in temperature space and time courses of > potential > > energy of each replica( one way is md.edr file??) > > As according to GROMACS tutorial, I used demux.pl script and got two > files > > replica_index.xvg and replica_temp.xvg. But I want to analyse a single > > replica trajectory in all temperatures ( temp. on y-axis) > > > > > > Thank you in advance.. > > > > Sundari > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD temperature_space
Hello Guys, Kindly suggest me something about my doubt. On Thu, May 3, 2018 at 5:19 PM, Sundari wrote: > Hello, > > I got the continuous trajectories by using demux. But now I am confused in > getting potential energy distribution of a single replica (similarly time > evolution of a replica (say replica_1) in temperature space). > I used edr file of original production data files, but I am not getting > what I want. I am attaching the temp.xvg file of one replica (say T= 315K > replica) > > Thank You.. > > On Thu, May 3, 2018 at 5:02 PM, Mark Abraham > wrote: > >> Hi, >> >> It sounds like you just want to use the original data, which you had >> before >> you ran the demux script. >> >> Mark >> >> On Thu, May 3, 2018 at 1:28 PM Sundari wrote: >> >> > Dear gromacs users, >> > >> > can anyone please suggest me that how we get the time evolution of a >> > replica (say replica_1) in temperature space and time courses of >> potential >> > energy of each replica( one way is md.edr file??) >> > As according to GROMACS tutorial, I used demux.pl script and got two >> files >> > replica_index.xvg and replica_temp.xvg. But I want to analyse a single >> > replica trajectory in all temperatures ( temp. on y-axis) >> > >> > >> > Thank you in advance.. >> > >> > Sundari >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to gmx-users-requ...@gromacs.org. >> > >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support >> /Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD temperature_space
Hi, Unfortunately nobody has implemented demux for the energy files. You could consider contributing a modification of demux.pl :-) Mark On Fri, May 4, 2018 at 8:42 AM Sundari wrote: > Hello Guys, > > Kindly suggest me something about my doubt. > > On Thu, May 3, 2018 at 5:19 PM, Sundari wrote: > > > Hello, > > > > I got the continuous trajectories by using demux. But now I am confused > in > > getting potential energy distribution of a single replica (similarly time > > evolution of a replica (say replica_1) in temperature space). > > I used edr file of original production data files, but I am not getting > > what I want. I am attaching the temp.xvg file of one replica (say T= 315K > > replica) > > > > Thank You.. > > > > On Thu, May 3, 2018 at 5:02 PM, Mark Abraham > > wrote: > > > >> Hi, > >> > >> It sounds like you just want to use the original data, which you had > >> before > >> you ran the demux script. > >> > >> Mark > >> > >> On Thu, May 3, 2018 at 1:28 PM Sundari wrote: > >> > >> > Dear gromacs users, > >> > > >> > can anyone please suggest me that how we get the time evolution of a > >> > replica (say replica_1) in temperature space and time courses of > >> potential > >> > energy of each replica( one way is md.edr file??) > >> > As according to GROMACS tutorial, I used demux.pl script and got two > >> files > >> > replica_index.xvg and replica_temp.xvg. But I want to analyse a > single > >> > replica trajectory in all temperatures ( temp. on y-axis) > >> > > >> > > >> > Thank you in advance.. > >> > > >> > Sundari > >> > -- > >> > Gromacs Users mailing list > >> > > >> > * Please search the archive at > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> > posting! > >> > > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > >> > * For (un)subscribe requests visit > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> > send a mail to gmx-users-requ...@gromacs.org. > >> > > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at http://www.gromacs.org/Support > >> /Mailing_Lists/GMX-Users_List before posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD tutorial
On Thu, Aug 21, 2014 at 8:01 AM, shahab shariati wrote: > Dear Mark > > Before, in following address you said: Google knows about two GROMACS REMD > tutorials. > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-January/086563.html > > Unfortunately, I could not find tutorials you mentioned. > You can find them here https://www.google.se/search?q=gromacs+remd+tutorials&oq=gromacs+remd+tutorials > > > > Also, in following address you said: I've added a section on > replica-exchange to > http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2007-December/031188.html > . > > Is this link active, now? I have no access to this link. > The webpage has been changed since then, see link from http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation Mark > > - > > I want to know Is there a tutorial for REMD like what is in > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/. > > Any help will highly appreciated. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD Plots
Hi Shan, I am not quite sure if you want to generate an REMD simulation mobility in temperature space for the 30 replicas. If that be the case, then you can use the data in the replica_temperature.xvg file to plot replica index vs REMD steps. The 1st column in the file corresponds to the REMD steps and 2nd to 31st correspond to the mobility of replicas 0 to 29. Hope this helps? cheers Joel On Wed, 9 Jan 2019 at 13:23, Shan Jayasinghe wrote: > Dear Gromacs users, > > How do we plot a graph for temperature vs swap step number using a REMD > simulation with 30 systems. I already generated the replica_temp.xvg and > replica_index.xvg files using demux.pl script. > > Thank you. > > Best Regards > Shan Jayasinghe > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Joel Baffour Awuah PhD Candidate *Institute for Frontier Materials* *Deakin University* *Waurn Ponds, 3126 VIC* *Australia +61450070635* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD Plots
Hi Joel, Thank you very much. On Wed, Jan 9, 2019 at 3:27 PM Joel Awuah wrote: > Hi Shan, > I am not quite sure if you want to generate an REMD simulation mobility in > temperature space for the 30 replicas. If that be the case, then you can > use the data in the replica_temperature.xvg file to plot replica index vs > REMD steps. The 1st column in the file corresponds to the REMD steps and > 2nd to 31st correspond to the mobility of replicas 0 to 29. > > Hope this helps? > > cheers > Joel > > > On Wed, 9 Jan 2019 at 13:23, Shan Jayasinghe > > wrote: > > > Dear Gromacs users, > > > > How do we plot a graph for temperature vs swap step number using a REMD > > simulation with 30 systems. I already generated the replica_temp.xvg and > > replica_index.xvg files using demux.pl script. > > > > Thank you. > > > > Best Regards > > Shan Jayasinghe > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > Joel Baffour Awuah > PhD Candidate > *Institute for Frontier Materials* > > *Deakin University* > *Waurn Ponds, 3126 VIC* > *Australia +61450070635* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Best Regards Shan Jayasinghe -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] remd error
This is an MPI / job scheduler error: you are requesting 2 nodes with
20 processes per node (=40 total), but starting 80 ranks.
--
Szilárd
On Thu, Jul 18, 2019 at 8:33 AM Bratin Kumar Das
<177cy500.bra...@nitk.edu.in> wrote:
>
> Hi,
>I am running remd simulation in gromacs-2016.5. After generating the
> multiple .tpr file in each directory by the following command
> *for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro -p
> topol.top -o remd$i.tpr -maxwarn 1; cd ..; done*
> I run *mpirun -np 80 gmx_mpi mdrun -s remd.tpr -multi 8 -replex 1000
> -reseed 175320 -deffnm remd_equil*
> It is giving the following error
> There are not enough slots available in the system to satisfy the 40 slots
> that were requested by the application:
> gmx_mpi
>
> Either request fewer slots for your application, or make more slots
> available
> for use.
> --
> --
> There are not enough slots available in the system to satisfy the 40 slots
> that were requested by the application:
> gmx_mpi
>
> Either request fewer slots for your application, or make more slots
> available
> for use.
> --
> I am not understanding the error. Any suggestion will be highly
> appriciated. The mdp file and the qsub.sh file is attached below
>
> qsub.sh...
> #! /bin/bash
> #PBS -V
> #PBS -l nodes=2:ppn=20
> #PBS -l walltime=48:00:00
> #PBS -N mdrun-serial
> #PBS -j oe
> #PBS -o output.log
> #PBS -e error.log
> #cd /home/bratin/Downloads/GROMACS/Gromacs_fibril
> cd $PBS_O_WORKDIR
> module load openmpi3.0.0
> module load gromacs-2016.5
> NP='cat $PBS_NODEFILE | wc -1'
> # mpirun --machinefile $PBS_PBS_NODEFILE -np $NP 'which gmx_mpi' mdrun -v
> -s nvt.tpr -deffnm nvt
> #/apps/gromacs-2016.5/bin/mpirun -np 8 gmx_mpi mdrun -v -s remd.tpr -multi
> 8 -replex 1000 -deffnm remd_out
> for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro -r
> em.gro -p topol.top -o remd$i.tpr -maxwarn 1; cd ..; done
>
> for i in {0..7}; do cd equil${i}; mpirun -np 40 gmx_mpi mdrun -v -s
> remd.tpr -multi 8 -replex 1000 -deffnm remd$i_out ; cd ..; done
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
> mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] remd error
Hi Szilard,
Thank you for your reply. I rectified as you said. For trial
purpose i took 8 nodes or 16 nodes... (-np 8) to text whether it is running
or not. I gave the following command to run remd
*mpirun -np 8 gmx_mpi_d mdrun -v -multi 8 -replex 1000 -deffnm remd*
After giving the command it is giving following error
Program: gmx mdrun, version 2018.4
Source file: src/gromacs/utility/futil.cpp (line 514)
MPI rank:0 (out of 32)
File input/output error:
remd0.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
I am not able to understand why it is coming
On Thu 25 Jul, 2019, 2:31 PM Szilárd Páll, wrote:
> This is an MPI / job scheduler error: you are requesting 2 nodes with
> 20 processes per node (=40 total), but starting 80 ranks.
> --
> Szilárd
>
> On Thu, Jul 18, 2019 at 8:33 AM Bratin Kumar Das
> <177cy500.bra...@nitk.edu.in> wrote:
> >
> > Hi,
> >I am running remd simulation in gromacs-2016.5. After generating the
> > multiple .tpr file in each directory by the following command
> > *for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro -p
> > topol.top -o remd$i.tpr -maxwarn 1; cd ..; done*
> > I run *mpirun -np 80 gmx_mpi mdrun -s remd.tpr -multi 8 -replex 1000
> > -reseed 175320 -deffnm remd_equil*
> > It is giving the following error
> > There are not enough slots available in the system to satisfy the 40
> slots
> > that were requested by the application:
> > gmx_mpi
> >
> > Either request fewer slots for your application, or make more slots
> > available
> > for use.
> >
> --
> >
> --
> > There are not enough slots available in the system to satisfy the 40
> slots
> > that were requested by the application:
> > gmx_mpi
> >
> > Either request fewer slots for your application, or make more slots
> > available
> > for use.
> >
> --
> > I am not understanding the error. Any suggestion will be highly
> > appriciated. The mdp file and the qsub.sh file is attached below
> >
> > qsub.sh...
> > #! /bin/bash
> > #PBS -V
> > #PBS -l nodes=2:ppn=20
> > #PBS -l walltime=48:00:00
> > #PBS -N mdrun-serial
> > #PBS -j oe
> > #PBS -o output.log
> > #PBS -e error.log
> > #cd /home/bratin/Downloads/GROMACS/Gromacs_fibril
> > cd $PBS_O_WORKDIR
> > module load openmpi3.0.0
> > module load gromacs-2016.5
> > NP='cat $PBS_NODEFILE | wc -1'
> > # mpirun --machinefile $PBS_PBS_NODEFILE -np $NP 'which gmx_mpi' mdrun -v
> > -s nvt.tpr -deffnm nvt
> > #/apps/gromacs-2016.5/bin/mpirun -np 8 gmx_mpi mdrun -v -s remd.tpr
> -multi
> > 8 -replex 1000 -deffnm remd_out
> > for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro -r
> > em.gro -p topol.top -o remd$i.tpr -maxwarn 1; cd ..; done
> >
> > for i in {0..7}; do cd equil${i}; mpirun -np 40 gmx_mpi mdrun -v -s
> > remd.tpr -multi 8 -replex 1000 -deffnm remd$i_out ; cd ..; done
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] remd error
On 7/29/19 7:55 AM, Bratin Kumar Das wrote:
Hi Szilard,
Thank you for your reply. I rectified as you said. For trial
purpose i took 8 nodes or 16 nodes... (-np 8) to text whether it is running
or not. I gave the following command to run remd
*mpirun -np 8 gmx_mpi_d mdrun -v -multi 8 -replex 1000 -deffnm remd*
After giving the command it is giving following error
Program: gmx mdrun, version 2018.4
Source file: src/gromacs/utility/futil.cpp (line 514)
MPI rank:0 (out of 32)
File input/output error:
remd0.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
I am not able to understand why it is coming
The error means the input file (remd0.tpr) does not exist in the working
directory.
-Justin
On Thu 25 Jul, 2019, 2:31 PM Szilárd Páll, wrote:
This is an MPI / job scheduler error: you are requesting 2 nodes with
20 processes per node (=40 total), but starting 80 ranks.
--
Szilárd
On Thu, Jul 18, 2019 at 8:33 AM Bratin Kumar Das
<177cy500.bra...@nitk.edu.in> wrote:
Hi,
I am running remd simulation in gromacs-2016.5. After generating the
multiple .tpr file in each directory by the following command
*for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro -p
topol.top -o remd$i.tpr -maxwarn 1; cd ..; done*
I run *mpirun -np 80 gmx_mpi mdrun -s remd.tpr -multi 8 -replex 1000
-reseed 175320 -deffnm remd_equil*
It is giving the following error
There are not enough slots available in the system to satisfy the 40
slots
that were requested by the application:
gmx_mpi
Either request fewer slots for your application, or make more slots
available
for use.
--
--
There are not enough slots available in the system to satisfy the 40
slots
that were requested by the application:
gmx_mpi
Either request fewer slots for your application, or make more slots
available
for use.
--
I am not understanding the error. Any suggestion will be highly
appriciated. The mdp file and the qsub.sh file is attached below
qsub.sh...
#! /bin/bash
#PBS -V
#PBS -l nodes=2:ppn=20
#PBS -l walltime=48:00:00
#PBS -N mdrun-serial
#PBS -j oe
#PBS -o output.log
#PBS -e error.log
#cd /home/bratin/Downloads/GROMACS/Gromacs_fibril
cd $PBS_O_WORKDIR
module load openmpi3.0.0
module load gromacs-2016.5
NP='cat $PBS_NODEFILE | wc -1'
# mpirun --machinefile $PBS_PBS_NODEFILE -np $NP 'which gmx_mpi' mdrun -v
-s nvt.tpr -deffnm nvt
#/apps/gromacs-2016.5/bin/mpirun -np 8 gmx_mpi mdrun -v -s remd.tpr
-multi
8 -replex 1000 -deffnm remd_out
for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro -r
em.gro -p topol.top -o remd$i.tpr -maxwarn 1; cd ..; done
for i in {0..7}; do cd equil${i}; mpirun -np 40 gmx_mpi mdrun -v -s
remd.tpr -multi 8 -replex 1000 -deffnm remd$i_out ; cd ..; done
--
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send a mail to gmx-users-requ...@gromacs.org.
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--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==
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Re: [gmx-users] remd error
Thank you
On Mon 29 Jul, 2019, 6:45 PM Justin Lemkul, wrote:
>
>
> On 7/29/19 7:55 AM, Bratin Kumar Das wrote:
> > Hi Szilard,
> > Thank you for your reply. I rectified as you said. For
> trial
> > purpose i took 8 nodes or 16 nodes... (-np 8) to text whether it is
> running
> > or not. I gave the following command to run remd
> > *mpirun -np 8 gmx_mpi_d mdrun -v -multi 8 -replex 1000 -deffnm remd*
> > After giving the command it is giving following error
> > Program: gmx mdrun, version 2018.4
> > Source file: src/gromacs/utility/futil.cpp (line 514)
> > MPI rank:0 (out of 32)
> >
> > File input/output error:
> > remd0.tpr
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > I am not able to understand why it is coming
>
> The error means the input file (remd0.tpr) does not exist in the working
> directory.
>
> -Justin
>
> >
> > On Thu 25 Jul, 2019, 2:31 PM Szilárd Páll,
> wrote:
> >
> >> This is an MPI / job scheduler error: you are requesting 2 nodes with
> >> 20 processes per node (=40 total), but starting 80 ranks.
> >> --
> >> Szilárd
> >>
> >> On Thu, Jul 18, 2019 at 8:33 AM Bratin Kumar Das
> >> <177cy500.bra...@nitk.edu.in> wrote:
> >>> Hi,
> >>> I am running remd simulation in gromacs-2016.5. After generating
> the
> >>> multiple .tpr file in each directory by the following command
> >>> *for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro
> -p
> >>> topol.top -o remd$i.tpr -maxwarn 1; cd ..; done*
> >>> I run *mpirun -np 80 gmx_mpi mdrun -s remd.tpr -multi 8 -replex 1000
> >>> -reseed 175320 -deffnm remd_equil*
> >>> It is giving the following error
> >>> There are not enough slots available in the system to satisfy the 40
> >> slots
> >>> that were requested by the application:
> >>>gmx_mpi
> >>>
> >>> Either request fewer slots for your application, or make more slots
> >>> available
> >>> for use.
> >>>
> >>
> --
> >>
> --
> >>> There are not enough slots available in the system to satisfy the 40
> >> slots
> >>> that were requested by the application:
> >>>gmx_mpi
> >>>
> >>> Either request fewer slots for your application, or make more slots
> >>> available
> >>> for use.
> >>>
> >>
> --
> >>> I am not understanding the error. Any suggestion will be highly
> >>> appriciated. The mdp file and the qsub.sh file is attached below
> >>>
> >>> qsub.sh...
> >>> #! /bin/bash
> >>> #PBS -V
> >>> #PBS -l nodes=2:ppn=20
> >>> #PBS -l walltime=48:00:00
> >>> #PBS -N mdrun-serial
> >>> #PBS -j oe
> >>> #PBS -o output.log
> >>> #PBS -e error.log
> >>> #cd /home/bratin/Downloads/GROMACS/Gromacs_fibril
> >>> cd $PBS_O_WORKDIR
> >>> module load openmpi3.0.0
> >>> module load gromacs-2016.5
> >>> NP='cat $PBS_NODEFILE | wc -1'
> >>> # mpirun --machinefile $PBS_PBS_NODEFILE -np $NP 'which gmx_mpi' mdrun
> -v
> >>> -s nvt.tpr -deffnm nvt
> >>> #/apps/gromacs-2016.5/bin/mpirun -np 8 gmx_mpi mdrun -v -s remd.tpr
> >> -multi
> >>> 8 -replex 1000 -deffnm remd_out
> >>> for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro
> -r
> >>> em.gro -p topol.top -o remd$i.tpr -maxwarn 1; cd ..; done
> >>>
> >>> for i in {0..7}; do cd equil${i}; mpirun -np 40 gmx_mpi mdrun -v -s
> >>> remd.tpr -multi 8 -replex 1000 -deffnm remd$i_out ; cd ..; done
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>> * For (un)subscribe requests visit
> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gro
Re: [gmx-users] REMD-error
Hi, We need to see your command line in order to have a chance of helping. Mark On Wed, 4 Sep 2019 at 05:46, Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Dear all, > I am running one REMD simulation with 65 replicas. I am using > 130 cores for the simulation. I am getting the following error. > > Fatal error: > Your choice of number of MPI ranks and amount of resources results in using > 16 > OpenMP threads per rank, which is most likely inefficient. The optimum is > usually between 1 and 6 threads per rank. If you want to run with this > setup, > specify the -ntomp option. But we suggest to change the number of MPI > ranks. > > when I am using -ntomp option ...it is throwing another error > > Fatal error: > Setting the number of thread-MPI ranks is only supported with thread-MPI > and > GROMACS was compiled without thread-MPI > > > while GROMACS is compiled with threated-MPI... > > plerase help me in this regard. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD-error
Respected Mark Abraham, The command-line and the job submission script is given below #!/bin/bash #SBATCH -n 130 # Number of cores #SBATCH -N 5 # no of nodes #SBATCH -t 0-20:00:00 # Runtime in D-HH:MM #SBATCH -p cpu # Partition to submit to #SBATCH -o hostname_%j.out # File to which STDOUT will be written #SBATCH -e hostname_%j.err # File to which STDERR will be written #loading gromacs module load gromacs/2018.4 #specifying work_dir WORKDIR=/home/chm_bratin/GMX_Projects/REMD/4wbu-REMD-inst-clust_1/stage-1 mpirun -np 130 gmx_mpi_d mdrun -v -s remd_nvt_next2.tpr -multidir equil0 equil1 equil2 equil3 equil4 equil5 equil6 equil7 equil8 equil9 equil10 equil11 equil12 equil13 equil14 equil15 equil16 equil17 equil18 equil19 equil20 equil21 equil22 equil23 equil24 equil25 equil26 equil27 equil28 equil29 equil30 equil31 equil32 equil33 equil34 equil35 equil36 equil37 equil38 equil39 equil40 equil41 equil42 equil43 equil44 equil45 equil46 equil47 equil48 equil49 equil50 equil51 equil52 equil53 equil54 equil55 equil56 equil57 equil58 equil59 equil60 equil61 equil62 equil63 equil64 -deffnm remd_nvt -cpi remd_nvt.cpt -append On Wed, Sep 4, 2019 at 2:13 PM Mark Abraham wrote: > Hi, > > We need to see your command line in order to have a chance of helping. > > Mark > > On Wed, 4 Sep 2019 at 05:46, Bratin Kumar Das <177cy500.bra...@nitk.edu.in > > > wrote: > > > Dear all, > > I am running one REMD simulation with 65 replicas. I am using > > 130 cores for the simulation. I am getting the following error. > > > > Fatal error: > > Your choice of number of MPI ranks and amount of resources results in > using > > 16 > > OpenMP threads per rank, which is most likely inefficient. The optimum is > > usually between 1 and 6 threads per rank. If you want to run with this > > setup, > > specify the -ntomp option. But we suggest to change the number of MPI > > ranks. > > > > when I am using -ntomp option ...it is throwing another error > > > > Fatal error: > > Setting the number of thread-MPI ranks is only supported with thread-MPI > > and > > GROMACS was compiled without thread-MPI > > > > > > while GROMACS is compiled with threated-MPI... > > > > plerase help me in this regard. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD-error
Hi, On Wed, 4 Sep 2019 at 10:47, Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Respected Mark Abraham, > The command-line and the job > submission script is given below > > #!/bin/bash > #SBATCH -n 130 # Number of cores > Per the docs, this is a guide to sbatch about how many (MPI) tasks you want to run. It's not a core request. #SBATCH -N 5 # no of nodes > This requires a certain number of nodes. So to implement both your instructions, MPI has to start 26 tasks per node. That would make sense if you had nodes with a multiple 26 cores. My guess is that your nodes have a multiple of 16 cores, based on the error message. MPI saw that you asked to allocate more tasks on cores than available cores, and decided not to set a number of OpenMP threads per MPI task, so that fell back on a default, which produced 16, which GROMACS can see doesn't make sense. If you want to use -N and -n, then you need to make a choice that makes sense for the number of cores per node. Easier might be to use -n 130 and -c 2 to express what I assume is your intent to have 2 cores per MPI task. Now slurm+MPI can pass that message along properly to OpenMP. Your other message about -ntomp can only have come from running gmx_mpi_d -ntmpi, so just a typo we don't need to worry about further. Mark #SBATCH -t 0-20:00:00 # Runtime in D-HH:MM > #SBATCH -p cpu # Partition to submit to > #SBATCH -o hostname_%j.out # File to which STDOUT will be written > #SBATCH -e hostname_%j.err # File to which STDERR will be written > #loading gromacs > module load gromacs/2018.4 > #specifying work_dir > WORKDIR=/home/chm_bratin/GMX_Projects/REMD/4wbu-REMD-inst-clust_1/stage-1 > > > mpirun -np 130 gmx_mpi_d mdrun -v -s remd_nvt_next2.tpr -multidir equil0 > equil1 equil2 equil3 equil4 equil5 equil6 equil7 equil8 equil9 equil10 > equil11 equil12 equil13 equil14 equil15 equil16 equil17 equil18 equil19 > equil20 equil21 equil22 equil23 equil24 equil25 equil26 equil27 equil28 > equil29 equil30 equil31 equil32 equil33 equil34 equil35 equil36 equil37 > equil38 equil39 equil40 equil41 equil42 equil43 equil44 equil45 equil46 > equil47 equil48 equil49 equil50 equil51 equil52 equil53 equil54 equil55 > equil56 equil57 equil58 equil59 equil60 equil61 equil62 equil63 equil64 > -deffnm remd_nvt -cpi remd_nvt.cpt -append > > On Wed, Sep 4, 2019 at 2:13 PM Mark Abraham > wrote: > > > Hi, > > > > We need to see your command line in order to have a chance of helping. > > > > Mark > > > > On Wed, 4 Sep 2019 at 05:46, Bratin Kumar Das < > 177cy500.bra...@nitk.edu.in > > > > > wrote: > > > > > Dear all, > > > I am running one REMD simulation with 65 replicas. I am > using > > > 130 cores for the simulation. I am getting the following error. > > > > > > Fatal error: > > > Your choice of number of MPI ranks and amount of resources results in > > using > > > 16 > > > OpenMP threads per rank, which is most likely inefficient. The optimum > is > > > usually between 1 and 6 threads per rank. If you want to run with this > > > setup, > > > specify the -ntomp option. But we suggest to change the number of MPI > > > ranks. > > > > > > when I am using -ntomp option ...it is throwing another error > > > > > > Fatal error: > > > Setting the number of thread-MPI ranks is only supported with > thread-MPI > > > and > > > GROMACS was compiled without thread-MPI > > > > > > > > > while GROMACS is compiled with threated-MPI... > > > > > > plerase help me in this regard. > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/m
Re: [gmx-users] REMD-error
Thank you for your email sir. On Wed, Sep 4, 2019 at 2:42 PM Mark Abraham wrote: > Hi, > > On Wed, 4 Sep 2019 at 10:47, Bratin Kumar Das <177cy500.bra...@nitk.edu.in > > > wrote: > > > Respected Mark Abraham, > > The command-line and the job > > submission script is given below > > > > #!/bin/bash > > #SBATCH -n 130 # Number of cores > > > > Per the docs, this is a guide to sbatch about how many (MPI) tasks you want > to run. It's not a core request. > > #SBATCH -N 5 # no of nodes > > > > This requires a certain number of nodes. So to implement both your > instructions, MPI has to start 26 tasks per node. That would make sense if > you had nodes with a multiple 26 cores. My guess is that your nodes have a > multiple of 16 cores, based on the error message. MPI saw that you asked to > allocate more tasks on cores than available cores, and decided not to set a > number of OpenMP threads per MPI task, so that fell back on a default, > which produced 16, which GROMACS can see doesn't make sense. > > If you want to use -N and -n, then you need to make a choice that makes > sense for the number of cores per node. Easier might be to use -n 130 and > -c 2 to express what I assume is your intent to have 2 cores per MPI task. > Now slurm+MPI can pass that message along properly to OpenMP. > > Your other message about -ntomp can only have come from running gmx_mpi_d > -ntmpi, so just a typo we don't need to worry about further. > > Mark > > #SBATCH -t 0-20:00:00 # Runtime in D-HH:MM > > #SBATCH -p cpu # Partition to submit to > > #SBATCH -o hostname_%j.out # File to which STDOUT will be written > > #SBATCH -e hostname_%j.err # File to which STDERR will be written > > #loading gromacs > > module load gromacs/2018.4 > > #specifying work_dir > > WORKDIR=/home/chm_bratin/GMX_Projects/REMD/4wbu-REMD-inst-clust_1/stage-1 > > > > > > mpirun -np 130 gmx_mpi_d mdrun -v -s remd_nvt_next2.tpr -multidir equil0 > > equil1 equil2 equil3 equil4 equil5 equil6 equil7 equil8 equil9 equil10 > > equil11 equil12 equil13 equil14 equil15 equil16 equil17 equil18 equil19 > > equil20 equil21 equil22 equil23 equil24 equil25 equil26 equil27 equil28 > > equil29 equil30 equil31 equil32 equil33 equil34 equil35 equil36 equil37 > > equil38 equil39 equil40 equil41 equil42 equil43 equil44 equil45 equil46 > > equil47 equil48 equil49 equil50 equil51 equil52 equil53 equil54 equil55 > > equil56 equil57 equil58 equil59 equil60 equil61 equil62 equil63 equil64 > > -deffnm remd_nvt -cpi remd_nvt.cpt -append > > > > On Wed, Sep 4, 2019 at 2:13 PM Mark Abraham > > wrote: > > > > > Hi, > > > > > > We need to see your command line in order to have a chance of helping. > > > > > > Mark > > > > > > On Wed, 4 Sep 2019 at 05:46, Bratin Kumar Das < > > 177cy500.bra...@nitk.edu.in > > > > > > > wrote: > > > > > > > Dear all, > > > > I am running one REMD simulation with 65 replicas. I am > > using > > > > 130 cores for the simulation. I am getting the following error. > > > > > > > > Fatal error: > > > > Your choice of number of MPI ranks and amount of resources results in > > > using > > > > 16 > > > > OpenMP threads per rank, which is most likely inefficient. The > optimum > > is > > > > usually between 1 and 6 threads per rank. If you want to run with > this > > > > setup, > > > > specify the -ntomp option. But we suggest to change the number of MPI > > > > ranks. > > > > > > > > when I am using -ntomp option ...it is throwing another error > > > > > > > > Fatal error: > > > > Setting the number of thread-MPI ranks is only supported with > > thread-MPI > > > > and > > > > GROMACS was compiled without thread-MPI > > > > > > > > > > > > while GROMACS is compiled with threated-MPI... > > > > > > > > plerase help me in this regard. > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailma
[gmx-users] REMD stall out
Hi, I continue to have trouble getting an REMD job to run. It never makes it to the point that it generates trajectory files but it never gives any error either. I have switched from a large TREMD with 72 replicas to the Plumed Hamiltonian method with only 6 replicas. Everything is now on one node and each replica has 6 cores. I've turned off the dynamic load balancing on this attempt per the recommendation from the Plumed site. Any ideas on how to troubleshoot? Thank you, Dan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD on GPU
Dear Gromacs users! I'd like to perform replica exchange simulation For this I've made bash script which create n folders like replica-298 replica-312 replica-323 replica-334 ... replica-N with all files needed for simulation considted of specified mdp file with different ref_t value No I'd like to launch this simulation using -multidir replica-298 replica-312 replica-323 replica-334 Unfortunately I've obtained Fatal error: mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support Does it possible to install mpirun on the existing Gromacs-4.6 built from source (without removing of the installed files)? Does it possible to run replica simulations in GPU supported mode ? Thanks for help, James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD Melting Curve
Dear Gromacs users, I have performed a REMD simulation with 12 replicas exponentially spaced between 260-420K. However, when I applied g_kinetics program to generate the melting curve, I got 161 values starting from 260K to 420K having the folded fraction reported at each temperature. My question is if I am applying 12 replicas exponentially spaced in the temperature range chosen, how could I get 161 values? Am I doing something wrong? Does g_kinetics in GROMACS use any smoothing function to generate the intermediate temperature and folded fraction values? Please suggest/advise. Atanu -- View this message in context: http://gromacs.5086.x6.nabble.com/REMD-Melting-Curve-tp5014920.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD exchange probabilities
On Sun, Mar 8, 2015 at 7:25 PM, Neha Gandhi wrote: > Dear list, > > Using an exchange probability of 0.25 and temperature range 293-370 K, I > calculated number of replicas using the server. However, when I did first > run and tried exchanging replicas every 500 steps (1 ps), I don't think the > exchange probabilities make sense in particular replicas 15 and 16. Replica > 15 has a low exchange ratio of 0.12 while replica 16 has a high exchange > ratio of 0.55. > This can be real. See literature from Nadler and Hansmann. If there's some temperature-dependent change in the range of available configurations (e.g. a phase transition), then you can have configuration(s) whose energy is such that they are accessible at one temperature and not at adjacent temperatures. Such replicas won't cross that temperature barrier until they have found a region of phase space that permits it. Such an ergodicity bottleneck suggests adding other replicas around that temperature, because you need flow over replica space to achieve the desired enhanced sampling. Repl average probabilities: > Repl 0123456789 10 11 12 > 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 > 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 > 43 44 45 46 47 > Repl .28 .28 .28 .28 .29 .28 .29 .29 .28 .29 .28 .28 .29 > .29 .29 .12 .55 .29 .29 .30 .30 .29 .29 .26 .32 .31 .30 .30 > .30 .30 .30 .31 .31 .31 .31 .31 .31 .31 .31 .31 .31 .31 .32 > .32 .32 .32 .33 > Repl number of exchanges: > Repl 0123456789 10 11 12 > 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 > 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 > 43 44 45 46 47 > Repl 2901 2954 2873 3017 3038 2910 3009 2993 2934 3002 2981 2999 2927 > 3038 3059 1229 5757 3056 3100 3136 3054 3053 3109 2743 3166 3097 3185 > 3161 3189 3133 3226 3261 3242 3229 3205 3249 3227 3221 3222 3326 3303 3309 > 3320 3373 3346 3474 > Repl average number of exchanges: > Repl 0123456789 10 11 12 > 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 > 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 > 43 44 45 46 47 > Repl .28 .28 .27 .29 .29 .28 .29 .29 .28 .29 .29 .29 .28 > .29 .29 .12 .55 .29 .30 .30 .29 .29 .30 .26 .32 .30 .30 .30 > .30 .31 .30 .31 .31 .31 .31 .31 .31 .31 .31 .31 .32 .32 .32 > .32 .32 .32 .33 > > > Below are the temperatures I have used. How do I manually edit temperatures > to get average exchange probabilities between 0.2-0.3? > The same way you set up the original set of temperatures - make an .mdp that has a temperature you want, equilibrate, and then insert it into the set of replicas before a new run. Your existing set of temperatures has one spacing of exactly one degree, and the rest seem to be exponential, so that looks funny. ref_t= 293293; reference temperature, one for each > group, in K > ref_t= 294.51 294.51; reference temperature, one for each > group, in K > ref_t= 296.03 296.03; reference temperature, one for each > group, in K > ref_t= 297.56 297.56; reference temperature, one for each > group, in K > ref_t= 299.09 299.09; reference temperature, one for each > group, in K > ref_t= 300.63 300.63; reference temperature, one for each > group, in K > ref_t= 302.18 302.18; reference temperature, one for each > group, in K > ref_t= 303.73 303.73; reference temperature, one for each > group, in K > ref_t= 305.29 305.29; reference temperature, one for each > group, in K > ref_t= 306.86 306.86; reference temperature, one for each > group, in K > ref_t= 308.43 308.43; reference temperature, one for each > group, in K > ref_t= 310.01 310.01; reference temperature, one for each > group, in K > ref_t= 311.60 311.60; reference temperature, one for each > group, in K > ref_t= 313.19 313.19; reference temperature, one for each > group, in K > ref_t= 314.79 314.79; reference temperature, one for each > group, in K > ref_t= 316.40 316.40; reference temperature, one for each > group, in K > ref_t= 318.63 318.63; reference temperature, one for each > group, in K > ref_t= 319.63 319.63; reference temperature, one for each > group, in K > ref_t= 321.26 321.26; reference temperature, one for each > group, in K > ref_t= 322.89 322.89; reference temperature, one for each > group, in K > ref_t= 324.52 324.52; reference temperature, one for each > group, in K > ref
Re: [gmx-users] REMD mdrun_mpi error
Hi, Do your individual replica .tpr files run correctly on their own? Mark On Mon, Jun 22, 2015 at 3:35 PM Nawel Mele wrote: > Dear gromacs users, > > I am trying to simulate a ligand using REMD method in explicit solvent with > the charmm force field. When I try to equilibrate my system I get this > error : > > Double sids (0, 1) for atom 26 > Double sids (0, 1) for atom 27 > Double sids (0, 1) for atom 28 > Double sids (0, 1) for atom 29 > Double sids (0, 1) for atom 30 > Double sids (0, 1) for atom 31 > Double sids (0, 1) for atom 32 > Double sids (0, 1) for atom 33 > Double sids (0, 1) for atom 34 > Double sids (0, 1) for atom 35 > Double sids (0, 1) for atom 36 > Double sids (0, 1) for atom 37 > Double sids (0, 1) for atom 38 > Double sids (0, 1) for atom 39 > Double sids (0, 1) for atom 40 > > --- > Program mdrun_mpi, VERSION 4.6.5 > Source code file: > /local/software/gromacs/4.6.5/source/gromacs-4.6.5/src/gmxlib/invblock.c, > line: 99 > > Fatal error: > Double entries in block structure. Item 53 is in blocks 1 and 0 > Cannot make an unambiguous inverse block. > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > > > *My mdp input file looks like this :* > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *title = CHARMM compound NVT equilibration define = > -DPOSRES ; position restrain the protein; Run > parametersintegrator = sd; leap-frog stochastic dynamics > integratornsteps = 100 ; 2 * 100 = 100 > psdt = 0.002 ; 2 fs; Output controlnstxout = > 500 ; save coordinates every 0.2 psnstvout = > 10; save velocities every 0.2 psnstenergy = 500 > ; save energies every 0.2 psnstlog = 500 ; update log > file every 0.2 ps; Bond parameterscontinuation= no; first > dynamics runconstraint_algorithm = SHAKE; holonomic constraints > constraints = h-bonds ; all bonds (even heavy atom-H bonds) > constrainedshake-tol = 0.1 ; relative tolerance for SHAKE; > Neighborsearchingns_type = grid ; search neighboring grid > cellsnstlist = 5 ; 10 fsrlist = 1.0 > ; short-range neighborlist cutoff (in nm)rcoulomb= 1.0 ; > short-range electrostatic cutoff (in nm)rvdw= 1.0 ; > short-range van der Waals cutoff (in nm); Electrostaticscoulombtype = > PME ; Particle Mesh Ewald for long-range > electrostaticspme_order = 4 ; Interpolation order for > PME. 4 equals cubic interpolationfourierspacing = 0.16 ; grid > spacing for FFT; Temperature coupling is on;tcoupl = V-rescale > ; modified Berendsen thermostattc-grps = LIG SOL ; two > coupling groups - more accuratetau_t = 1.0 1.0 ; time > constant, in psref_t = X X ; reference > temperature, one for each group, in K;Langevin dynamicsbd-fric = 0 > ; ;Brownian dynamics friction coefficient. ld-seed > =-1;;pseudo random seed is used; Pressure coupling is > offpcoupl = no; no pressure coupling in NVT; Periodic > boundary conditionspbc = xyz ; 3-D PBC; Dispersion > correctionDispCorr= EnerPres ; account for cut-off vdW scheme; > Velocity generationgen_vel = yes ; assign velocities from > Maxwell distributiongen_temp= 0.0 ; temperature for > Maxwell distributiongen_seed= -1; generate a random > seed* > > > *And my input file to run it in parallel looks like that:* > > > > > > > > > > > *#!/bin/bash#PBS -l nodes=3:ppn=16#PBS -l walltime=00:10:00#PBS -o > zzz.qsub.out#PBS -e zzz.qsub.errmodule load openmpi module load > gromacs/4.6.5mpirun -np 48 mdrun_mpi -s eq_.tpr -multi 48 -replex 10 > >& faillog-X.log* > > > Does anyone have seen this issue before?? > > Many thanks, > -- > > Nawel Mele, PhD Research Student > > Jonathan Essex Group, School of Chemistry > > University of Southampton, Highfield > > Southampton, SO17 1BJ > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.
Re: [gmx-users] REMD mdrun_mpi error
Hi Mark,
I tried to run an individual tpr file and it crashed:
Double sids (0, 1) for atom 26
Double sids (0, 1) for atom 27
Double sids (0, 1) for atom 28
Double sids (0, 1) for atom 29
Double sids (0, 1) for atom 30
Double sids (0, 1) for atom 31
Double sids (0, 1) for atom 32
Double sids (0, 1) for atom 33
Double sids (0, 1) for atom 34
Double sids (0, 1) for atom 35
Double sids (0, 1) for atom 36
Double sids (0, 1) for atom 37
Double sids (0, 1) for atom 38
Double sids (0, 1) for atom 39
Double sids (0, 1) for atom 40
---
Program mdrun, VERSION 4.6.5
Source code file:
/local/software/gromacs/4.6.5/source/gromacs-4.6.5/src/gmxlib/invblock.c,
line: 99
Fatal error:
Double entries in block structure. Item 53 is in blocks 1 and 0
Cannot make an unambiguous inverse block.
To create my tpr files I useda bash script like this:
*#!/bin/bash -fnrep=`wc temperatures.dat | awk '{print $1}'`echo
$nrepcount=0count2=-1for TEMP in `cat temperatures.dat`do let count2+=1
REP=`printf "%03d" $count2` REPBIS=`printf "%d" $count2` echo
"TEMPERATURE: $TEMP K ==> FILE: nvt_$REP.mdp" sed "s/X/$TEMP/g"
nvt.mdp > nvt_$REP.mdp grompp -f nvt_$REP.mdp -c min.gro -p topol.top -o
eq_$REPBIS.tpr -maxwarn 1 rm -f tempdoneecho "N REPLICAS = $nrep"echo "
Done."*
Nawel
2015-06-23 11:47 GMT+01:00 Mark Abraham :
> Hi,
>
> Do your individual replica .tpr files run correctly on their own?
>
> Mark
>
> On Mon, Jun 22, 2015 at 3:35 PM Nawel Mele wrote:
>
> > Dear gromacs users,
> >
> > I am trying to simulate a ligand using REMD method in explicit solvent
> with
> > the charmm force field. When I try to equilibrate my system I get this
> > error :
> >
> > Double sids (0, 1) for atom 26
> > Double sids (0, 1) for atom 27
> > Double sids (0, 1) for atom 28
> > Double sids (0, 1) for atom 29
> > Double sids (0, 1) for atom 30
> > Double sids (0, 1) for atom 31
> > Double sids (0, 1) for atom 32
> > Double sids (0, 1) for atom 33
> > Double sids (0, 1) for atom 34
> > Double sids (0, 1) for atom 35
> > Double sids (0, 1) for atom 36
> > Double sids (0, 1) for atom 37
> > Double sids (0, 1) for atom 38
> > Double sids (0, 1) for atom 39
> > Double sids (0, 1) for atom 40
> >
> > ---
> > Program mdrun_mpi, VERSION 4.6.5
> > Source code file:
> > /local/software/gromacs/4.6.5/source/gromacs-4.6.5/src/gmxlib/invblock.c,
> > line: 99
> >
> > Fatal error:
> > Double entries in block structure. Item 53 is in blocks 1 and 0
> > Cannot make an unambiguous inverse block.
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> >
> >
> > *My mdp input file looks like this :*
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > *title = CHARMM compound NVT equilibration define =
> > -DPOSRES ; position restrain the protein; Run
> > parametersintegrator = sd; leap-frog stochastic dynamics
> > integratornsteps = 100 ; 2 * 100 = 100
> > psdt = 0.002 ; 2 fs; Output controlnstxout =
> > 500 ; save coordinates every 0.2 psnstvout =
> > 10; save velocities every 0.2 psnstenergy = 500
> > ; save energies every 0.2 psnstlog = 500 ; update log
> > file every 0.2 ps; Bond parameterscontinuation= no; first
> > dynamics runconstraint_algorithm = SHAKE; holonomic constraints
> > constraints = h-bonds ; all bonds (even heavy atom-H bonds)
> > constrainedshake-tol = 0.1 ; relative tolerance for
> SHAKE;
> > Neighborsearchingns_type = grid ; search neighboring
> grid
> > cellsnstlist = 5 ; 10 fsrlist = 1.0
> > ; short-range neighborlist cutoff (in nm)rcoulomb= 1.0
> ;
> > short-range electrostatic cutoff (in nm)rvdw= 1.0 ;
> > short-range van der Waals cutoff (in nm); Electrostaticscoulombtype =
> > PME ; Particle Mesh Ewald for long-range
> > electrostaticspme_order = 4 ; Interpolation order for
> > PME. 4 equals cubic interpolationfourierspacing = 0.16 ; grid
> > spacing for FFT; Temperature coupling is on;tcoupl = V-rescale
> > ; modified Berendsen thermostattc-grps = LIG SOL ; two
> > coupling groups - more accuratetau_t = 1.0 1.0 ; time
> > constant, in psref_t = X X ; reference
> > temperature, one for each group, in K;Langevin dynamicsbd-fric =
> 0
> > ; ;Brownian dynamics friction coefficient. ld-seed
> > =-1;;pseudo random seed is used; Pressure coupling is
> > offpcoupl = no; no
[gmx-users] REMD with different structures
Hi I am trying to do NVT REMD simulations with gromacs. I have 60 replicas and each of them have different starting structure . The starting structures have same number of atoms but slightly different volume and pressure. I was able to run these simulations but I want to know if having different volume and pressure is affecting the exchange probability, and if it does, is it being included in the gromacs REMD simulations ? Please suggest a method to verify it . -- Regards Ruchi Lohia Graduate Student -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD system blowing up
Hi all, I would like to know if there is a way to figure out which of the replica is exploding during REMD simulation? I am running REMD for 54 replicas and the system is exploding with just one step14495b.pdb and step14495c.pdb files. Does this mean there is just one replica that is exploding? Does this also have to do with the temperature? The equilibration was carried out for 600 ps and the individual replicas have no issues. Awaiting response. Thanks! Nisha -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD of IDPs
Dear Yanhua, To my knowledge (prior to gromacs 5.X at least), there are no gromacs tools able to turn a sequence into a PDB. The user must take care of that pre-processing on his/her own. I work with IDPs quite a lot, so what I can tell you is what I usually do. I take my fasta sequence and use PyMOL to construct the PDB. Then I'm able to feed the PDB to pdb2gmx. *I'm sure there are a million different ways of doing this, given that there are so many different protein modelling tools out there.* Here's one example using Histatin 5. - On PyMOL's command line type the following (without the quotation marks): "for aa in "AKRHHGYKRKFH": cmd._alt(string.lower(aa))" - This builds a fully stretched Histatin 5 3D model which can be exported as PDB. - Make sure to use "-ignh" on pdb2gmx, as the resulting hydrogen atom names are usually incompatible with the force fields I routinely use. - It's also a good idea to use "-renum" on pdb2gmx as for some reason PyMOL exports the PDB with residue numberings starting from no. 2. Cheers, João On Fri, Apr 8, 2016 at 4:14 AM, YanhuaOuyang <15901283...@163.com> wrote: > Hi, I have a sequence of an intrinsically disordered protein, I have no > idea how to start my REMD with gromacs. e.g. how to convert my sequence > into a pdb file > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD of IDPs
Dear Yanhua, Converting a sequence into a structure is itself an "open" problem in computational biology/biophysics. There are ways to generate potential structures if you also happen to have some restraints from NMR or other experiments (small-angle scattering or CD-Spectra) noted in the literature, but getting to the "native" fold is very challenging. One program that tries to address the sequence to structure problem is Rosetta ( http://robetta.bakerlab.org/ ). If you have a short IDP fragment (less than 20 residues), one thing you can do it use something like Schrodinger's Maestro program (its free from their webpage www.schrodinger.com) and use the molecule builder to "grow" the chain as a random coil (random phi-psi placement), save the PDB from it and then run MD at high temp to relax the structure into a potential starting structure. If it is longer, the IDP may have small structural segments (the chain is dominated by disorder but may have short-lived, meta-stable, secondary structure regions) in which case you can either try to build the molecule with a corresponding secondary structure distribution (using Maestro) or try using Rosetta and refine with energy minimization. Good Luck! === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of João Henriques Sent: Friday, April 08, 2016 3:51 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] REMD of IDPs Dear Yanhua, To my knowledge (prior to gromacs 5.X at least), there are no gromacs tools able to turn a sequence into a PDB. The user must take care of that pre-processing on his/her own. I work with IDPs quite a lot, so what I can tell you is what I usually do. I take my fasta sequence and use PyMOL to construct the PDB. Then I'm able to feed the PDB to pdb2gmx. *I'm sure there are a million different ways of doing this, given that there are so many different protein modelling tools out there.* Here's one example using Histatin 5. - On PyMOL's command line type the following (without the quotation marks): "for aa in "AKRHHGYKRKFH": cmd._alt(string.lower(aa))" - This builds a fully stretched Histatin 5 3D model which can be exported as PDB. - Make sure to use "-ignh" on pdb2gmx, as the resulting hydrogen atom names are usually incompatible with the force fields I routinely use. - It's also a good idea to use "-renum" on pdb2gmx as for some reason PyMOL exports the PDB with residue numberings starting from no. 2. Cheers, João On Fri, Apr 8, 2016 at 4:14 AM, YanhuaOuyang <15901283...@163.com> wrote: > Hi, I have a sequence of an intrinsically disordered protein, I have no > idea how to start my REMD with gromacs. e.g. how to convert my sequence > into a pdb file > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD of IDPs
One small remark to Micholas' email: - Make sure the simulation box is big enough to allow the IDP to fully stretch without interacting with its periodic image(s). This is non-trivial if you build your system from a random coil. That's why I start from a fully stretched conformation instead of a more representative conformation of the system. Much easier to control and the time it takes to get to a "meaningful" conformation is minimal. /J On Fri, Apr 8, 2016 at 2:10 PM, Smith, Micholas D. wrote: > Dear Yanhua, > > Converting a sequence into a structure is itself an "open" problem in > computational biology/biophysics. There are ways to generate potential > structures if you also happen to have some restraints from NMR or other > experiments (small-angle scattering or CD-Spectra) noted in the literature, > but getting to the "native" fold is very challenging. One program that > tries to address the sequence to structure problem is Rosetta ( > http://robetta.bakerlab.org/ ). > > If you have a short IDP fragment (less than 20 residues), one thing you > can do it use something like Schrodinger's Maestro program (its free from > their webpage www.schrodinger.com) and use the molecule builder to "grow" > the chain as a random coil (random phi-psi placement), save the PDB from it > and then run MD at high temp to relax the structure into a potential > starting structure. If it is longer, the IDP may have small structural > segments (the chain is dominated by disorder but may have short-lived, > meta-stable, secondary structure regions) in which case you can either try > to build the molecule with a corresponding secondary structure distribution > (using Maestro) or try using Rosetta and refine with energy minimization. > > Good Luck! > > === > Micholas Dean Smith, PhD. > Post-doctoral Research Associate > University of Tennessee/Oak Ridge National Laboratory > Center for Molecular Biophysics > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of João > Henriques > Sent: Friday, April 08, 2016 3:51 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] REMD of IDPs > > Dear Yanhua, > > To my knowledge (prior to gromacs 5.X at least), there are no gromacs > tools able to turn a sequence into a PDB. The user must take care of that > pre-processing on his/her own. I work with IDPs quite a lot, so what I can > tell you is what I usually do. I take my fasta sequence and use PyMOL to > construct the PDB. Then I'm able to feed the PDB to pdb2gmx. > > *I'm sure there are a million different ways of doing this, given that > there are so many different protein modelling tools out there.* > > Here's one example using Histatin 5. > > - On PyMOL's command line type the following (without the quotation marks): > "for aa in "AKRHHGYKRKFH": cmd._alt(string.lower(aa))" > > - This builds a fully stretched Histatin 5 3D model which can be exported > as PDB. > > - Make sure to use "-ignh" on pdb2gmx, as the resulting hydrogen atom names > are usually incompatible with the force fields I routinely use. > > - It's also a good idea to use "-renum" on pdb2gmx as for some reason PyMOL > exports the PDB with residue numberings starting from no. 2. > > Cheers, > João > > > On Fri, Apr 8, 2016 at 4:14 AM, YanhuaOuyang <15901283...@163.com> wrote: > > > Hi, I have a sequence of an intrinsically disordered protein, I have no > > idea how to start my REMD with gromacs. e.g. how to convert my sequence > > into a pdb file > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX
Re: [gmx-users] REMD of IDPs
Very good point from João. Always remember to check that your box length is big enough! === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of João Henriques Sent: Friday, April 08, 2016 8:24 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] REMD of IDPs One small remark to Micholas' email: - Make sure the simulation box is big enough to allow the IDP to fully stretch without interacting with its periodic image(s). This is non-trivial if you build your system from a random coil. That's why I start from a fully stretched conformation instead of a more representative conformation of the system. Much easier to control and the time it takes to get to a "meaningful" conformation is minimal. /J On Fri, Apr 8, 2016 at 2:10 PM, Smith, Micholas D. wrote: > Dear Yanhua, > > Converting a sequence into a structure is itself an "open" problem in > computational biology/biophysics. There are ways to generate potential > structures if you also happen to have some restraints from NMR or other > experiments (small-angle scattering or CD-Spectra) noted in the literature, > but getting to the "native" fold is very challenging. One program that > tries to address the sequence to structure problem is Rosetta ( > http://robetta.bakerlab.org/ ). > > If you have a short IDP fragment (less than 20 residues), one thing you > can do it use something like Schrodinger's Maestro program (its free from > their webpage www.schrodinger.com) and use the molecule builder to "grow" > the chain as a random coil (random phi-psi placement), save the PDB from it > and then run MD at high temp to relax the structure into a potential > starting structure. If it is longer, the IDP may have small structural > segments (the chain is dominated by disorder but may have short-lived, > meta-stable, secondary structure regions) in which case you can either try > to build the molecule with a corresponding secondary structure distribution > (using Maestro) or try using Rosetta and refine with energy minimization. > > Good Luck! > > === > Micholas Dean Smith, PhD. > Post-doctoral Research Associate > University of Tennessee/Oak Ridge National Laboratory > Center for Molecular Biophysics > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of João > Henriques > Sent: Friday, April 08, 2016 3:51 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] REMD of IDPs > > Dear Yanhua, > > To my knowledge (prior to gromacs 5.X at least), there are no gromacs > tools able to turn a sequence into a PDB. The user must take care of that > pre-processing on his/her own. I work with IDPs quite a lot, so what I can > tell you is what I usually do. I take my fasta sequence and use PyMOL to > construct the PDB. Then I'm able to feed the PDB to pdb2gmx. > > *I'm sure there are a million different ways of doing this, given that > there are so many different protein modelling tools out there.* > > Here's one example using Histatin 5. > > - On PyMOL's command line type the following (without the quotation marks): > "for aa in "AKRHHGYKRKFH": cmd._alt(string.lower(aa))" > > - This builds a fully stretched Histatin 5 3D model which can be exported > as PDB. > > - Make sure to use "-ignh" on pdb2gmx, as the resulting hydrogen atom names > are usually incompatible with the force fields I routinely use. > > - It's also a good idea to use "-renum" on pdb2gmx as for some reason PyMOL > exports the PDB with residue numberings starting from no. 2. > > Cheers, > João > > > On Fri, Apr 8, 2016 at 4:14 AM, YanhuaOuyang <15901283...@163.com> wrote: > > > Hi, I have a sequence of an intrinsically disordered protein, I have no > > idea how to start my REMD with gromacs. e.g. how to convert my sequence > > into a pdb file > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Pl
[gmx-users] REMD ensemble of states
Hi, I conducted REMD, and extracted the trajectories via trjcat -f *.trr -demux replica_index.xvg And now I was wondering which *.xtc file is the ensemble of states at the baseline replica (lowest temperature replica). Intuitively my guess is that the numbers in the names of *_trajout.xtc files correspond to the replica numbers starting from the baseline, and hence 0_trajout.xtc is the ensemble of states at the baseline replica, but I may be wrong. Please suggest. Thank you, Tigran -- Tigran M. Abramyan, Ph.D. Postdoctoral Fellow, Computational Biophysics & Molecular Design Center for Integrative Chemical Biology and Drug Discovery Eshelman School of Pharmacy University of North Carolina at Chapel Hill Chapel Hill, NC 27599-7363 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD implicit solvent
Hi, Did you try to debug your setup by running a normal single-replica simulation first? Mark On Fri, Jan 5, 2018 at 12:12 PM Urszula Uciechowska < urszula.uciechow...@biotech.ug.edu.pl> wrote: > > > Dear gromacs users, > > I am trying to run REMD simulations using 4.5.5 version (implicit > solvent). The MD procedure: > > pdb2gmx -f prot.pdb -o prot.gro -q prot.pdb -ignh -ss. > > The input for minimization step: > > ; Run control parameters > integrator = cg > nsteps = 800 > vdwtype = cut-off > coulombtype = cut-off > ;cutoff-scheme= group > pbc = no > periodic_molecules = no > nstlist = 10 > ns_type = grid > rlist= 1.0 > rcoulomb = 1.6 > rvdw = 1.6 > comm-mode= Angular > nstcomm = 10 > ; > ;Energy minimizing stuff > ; > emtol= 100.0 > nstcgsteep = 2 > emstep = 0.01 > ; > ;Relative dielectric constant for the medium and the reaction field > epsilon_r= 1 > epsilon_rf = 1 > ; > ; Implicit solvent > ; > implicit_solvent = GBSA > gb_algorithm = OBC ;Still HCT OBC > nstgbradii = 1.0 > rgbradii = 1.0 ; [nm] Cut-off for the calculation of > the Born radii. Currently must be equal to rlist > gb_epsilon_solvent = 80 ; Dielectric constant for the implicit > solvent > gb_saltconc = 0; Salt concentration for implicit > solvent models, currently not used > sa_algorithm = Ace-approximation > sa_surface_tension = 2.05016 ; Surface tension (kJ/mol/nm^2) for > the SA (nonpolar surface) part of GBSA. The value -1 will set default > value for Still/HCT/OBC GB-models. > > and it finished without errors. > > The problem is with equilibration step. The input file that I used is: > > ; MD CONTROL OPTIONS > integrator = md > dt = 0.002 > nsteps = 5 ; 10 ns > init_step = 0; For exact run continuation or > redoing part of a run > comm-mode = Angular ; mode for center of mass motion > removal > nstcomm = 10 ; number of steps for center of > mass motion removal > > ; OUTPUT CONTROL OPTIONS > ; Output frequency for coords (x), velocities (v) and forces (f) > nstxout = 1000 > nstvout = 1000 > nstfout = 1000 > > ; Output frequency for energies to log file and energy file > nstlog = 1000 > nstcalcenergy= 10 > nstenergy= 1000 > > ; Neighbor searching and Electrostatitcs > vdwtype = cut-off > coulombtype = cut-off > ;cutoff-scheme= group > pbc = no > periodic_molecules = no > nstlist = 5 > ns_type = grid > rlist= 1.0 > rcoulomb = 1.6 > rvdw = 1.0 > ; Selection of energy groups > energygrps = fixed not_fixed > freezegrps = fixed not_fixed > freezedim= Y Y Y N N N > > ;Relative dielectric constant for the medium and the reaction field > epsilon_r= 1 > epsilon_rf = 1 > > ; Temperutare coupling > tcoupl = v-rescale > tc_grps = fixed not_fixed > tau_t= 0.01 0.01 > ;nst_couple = 5 > ref_t= 300.00 300.00 > > ; Pressure coupling > pcoupl = no > ;pcoupletype = isotropic > tau_p= 1.0 > ;compressiblity = 4.5e-5 > ref_p= 1.0 > gen_vel = yes > gen_temp = 300.00 300.00 > gen_seed = -1 > constraints = h-bonds > > > ; Implicit solvent > implicit_solvent = GBSA > gb_algorithm = Still ; HCT ; OBC > nstgbradii = 1.0 > rgbradii = 1.0 ; [nm] Cut-off for the calculation > of the Born radii. Currently must be equal to rlist > gb_epsilon_solvent = 80 ; Dielectric constant for the > implicit solvent > gb_saltconc = 0; Salt concentration for implicit > solvent models, currently not used > sa_algorithm = Ace-approximation > sa_surface_tension = 2.05016 ; Surface tension (kJ/mol/nm^2) > for the SA (nonpolar surface) part of GBSA. The value -1 will set default > value for Still/HCT/OBC GB-models. > > > mdrun -v -multidir eq_[12345678] > > The error that I obtained is: > > Fatal error: > A charge group moved too far between two domain decomposition steps > This usually means that your system is not well equilibrated > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > > I do n
Re: [gmx-users] REMD implicit solvent
Hi, I just run a normal single-replica. Now the error that I have is: Program mdrun_mpi, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Any suggestions? What can I do to run it? Thanks Ula > Hi, > > Did you try to debug your setup by running a normal single-replica > simulation first? > > Mark > > On Fri, Jan 5, 2018 at 12:12 PM Urszula Uciechowska < > urszula.uciechow...@biotech.ug.edu.pl> wrote: > >> >> >> Dear gromacs users, >> >> I am trying to run REMD simulations using 4.5.5 version (implicit >> solvent). The MD procedure: >> >> pdb2gmx -f prot.pdb -o prot.gro -q prot.pdb -ignh -ss. >> >> The input for minimization step: >> >> ; Run control parameters >> integrator = cg >> nsteps = 800 >> vdwtype = cut-off >> coulombtype = cut-off >> ;cutoff-scheme= group >> pbc = no >> periodic_molecules = no >> nstlist = 10 >> ns_type = grid >> rlist= 1.0 >> rcoulomb = 1.6 >> rvdw = 1.6 >> comm-mode= Angular >> nstcomm = 10 >> ; >> ;Energy minimizing stuff >> ; >> emtol= 100.0 >> nstcgsteep = 2 >> emstep = 0.01 >> ; >> ;Relative dielectric constant for the medium and the reaction field >> epsilon_r= 1 >> epsilon_rf = 1 >> ; >> ; Implicit solvent >> ; >> implicit_solvent = GBSA >> gb_algorithm = OBC ;Still HCT OBC >> nstgbradii = 1.0 >> rgbradii = 1.0 ; [nm] Cut-off for the calculation >> of >> the Born radii. Currently must be equal to rlist >> gb_epsilon_solvent = 80 ; Dielectric constant for the >> implicit >> solvent >> gb_saltconc = 0; Salt concentration for implicit >> solvent models, currently not used >> sa_algorithm = Ace-approximation >> sa_surface_tension = 2.05016 ; Surface tension (kJ/mol/nm^2) for >> the SA (nonpolar surface) part of GBSA. The value -1 will set default >> value for Still/HCT/OBC GB-models. >> >> and it finished without errors. >> >> The problem is with equilibration step. The input file that I used is: >> >> ; MD CONTROL OPTIONS >> integrator = md >> dt = 0.002 >> nsteps = 5 ; 10 ns >> init_step = 0; For exact run continuation or >> redoing part of a run >> comm-mode = Angular ; mode for center of mass motion >> removal >> nstcomm = 10 ; number of steps for center of >> mass motion removal >> >> ; OUTPUT CONTROL OPTIONS >> ; Output frequency for coords (x), velocities (v) and forces (f) >> nstxout = 1000 >> nstvout = 1000 >> nstfout = 1000 >> >> ; Output frequency for energies to log file and energy file >> nstlog = 1000 >> nstcalcenergy= 10 >> nstenergy= 1000 >> >> ; Neighbor searching and Electrostatitcs >> vdwtype = cut-off >> coulombtype = cut-off >> ;cutoff-scheme= group >> pbc = no >> periodic_molecules = no >> nstlist = 5 >> ns_type = grid >> rlist= 1.0 >> rcoulomb = 1.6 >> rvdw = 1.0 >> ; Selection of energy groups >> energygrps = fixed not_fixed >> freezegrps = fixed not_fixed >> freezedim= Y Y Y N N N >> >> ;Relative dielectric constant for the medium and the reaction field >> epsilon_r= 1 >> epsilon_rf = 1 >> >> ; Temperutare coupling >> tcoupl = v-rescale >> tc_grps = fixed not_fixed >> tau_t= 0.01 0.01 >> ;nst_couple = 5 >> ref_t= 300.00 300.00 >> >> ; Pressure coupling >> pcoupl = no >> ;pcoupletype = isotropic >> tau_p= 1.0 >> ;compressiblity = 4.5e-5 >> ref_p= 1.0 >> gen_vel = yes >> gen_temp = 300.00 300.00 >> gen_seed = -1 >> constraints = h-bonds >> >> >> ; Implicit solvent >> implicit_solvent = GBSA >> gb_algorithm = Still ; HCT ; OBC >> nstgbradii = 1.0 >> rgbradii = 1.0 ; [nm] Cut-off for the >> calculation >> of the Born radii. Currently must be equal to rlist >> gb_epsilon_solvent = 80 ; Dielectric constant for the >> implicit solvent >> gb_saltconc = 0; Salt concentration for >> implicit >> solvent models, currently not used >> sa_algorithm = Ace-approx
Re: [gmx-users] REMD implicit solvent
Hello, From my experience, the domain decomposition is not compatible with implicit solvent, you have to switch to particle decomposition for the simulations. All the best, Qinghua On 01/05/2018 12:40 PM, Urszula Uciechowska wrote: Hi, I just run a normal single-replica. Now the error that I have is: Program mdrun_mpi, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Any suggestions? What can I do to run it? Thanks Ula Hi, Did you try to debug your setup by running a normal single-replica simulation first? Mark On Fri, Jan 5, 2018 at 12:12 PM Urszula Uciechowska < urszula.uciechow...@biotech.ug.edu.pl> wrote: Dear gromacs users, I am trying to run REMD simulations using 4.5.5 version (implicit solvent). The MD procedure: pdb2gmx -f prot.pdb -o prot.gro -q prot.pdb -ignh -ss. The input for minimization step: ; Run control parameters integrator = cg nsteps = 800 vdwtype = cut-off coulombtype = cut-off ;cutoff-scheme= group pbc = no periodic_molecules = no nstlist = 10 ns_type = grid rlist= 1.0 rcoulomb = 1.6 rvdw = 1.6 comm-mode= Angular nstcomm = 10 ; ;Energy minimizing stuff ; emtol= 100.0 nstcgsteep = 2 emstep = 0.01 ; ;Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; ; Implicit solvent ; implicit_solvent = GBSA gb_algorithm = OBC ;Still HCT OBC nstgbradii = 1.0 rgbradii = 1.0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent gb_saltconc = 0; Salt concentration for implicit solvent models, currently not used sa_algorithm = Ace-approximation sa_surface_tension = 2.05016 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA. The value -1 will set default value for Still/HCT/OBC GB-models. and it finished without errors. The problem is with equilibration step. The input file that I used is: ; MD CONTROL OPTIONS integrator = md dt = 0.002 nsteps = 5 ; 10 ns init_step = 0; For exact run continuation or redoing part of a run comm-mode = Angular ; mode for center of mass motion removal nstcomm = 10 ; number of steps for center of mass motion removal ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency for energies to log file and energy file nstlog = 1000 nstcalcenergy= 10 nstenergy= 1000 ; Neighbor searching and Electrostatitcs vdwtype = cut-off coulombtype = cut-off ;cutoff-scheme= group pbc = no periodic_molecules = no nstlist = 5 ns_type = grid rlist= 1.0 rcoulomb = 1.6 rvdw = 1.0 ; Selection of energy groups energygrps = fixed not_fixed freezegrps = fixed not_fixed freezedim= Y Y Y N N N ;Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Temperutare coupling tcoupl = v-rescale tc_grps = fixed not_fixed tau_t= 0.01 0.01 ;nst_couple = 5 ref_t= 300.00 300.00 ; Pressure coupling pcoupl = no ;pcoupletype = isotropic tau_p= 1.0 ;compressiblity = 4.5e-5 ref_p= 1.0 gen_vel = yes gen_temp = 300.00 300.00 gen_seed = -1 constraints = h-bonds ; Implicit solvent implicit_solvent = GBSA gb_algorithm = Still ; HCT ; OBC nstgbradii = 1.0 rgbradii = 1.0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent gb_saltconc = 0; Salt concentration for implicit solvent models, currently not used sa_algorithm = Ace-approximation sa_surface_tension = 2.05016 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA. The value -1 will set default valu
Re: [gmx-users] REMD implicit solvent
Hi, I should run it by using mdrun_mpi? best Urszula > Hello, > > From my experience, the domain decomposition is not compatible with > implicit solvent, you have to switch > to particle decomposition for the simulations. > > > All the best, > Qinghua > > On 01/05/2018 12:40 PM, Urszula Uciechowska wrote: >> Hi, >> >> I just run a normal single-replica. Now the error that I have is: >> >> Program mdrun_mpi, VERSION 4.5.5 >> Source code file: domdec.c, line: 3266 >> >> Software inconsistency error: >> Inconsistent DD boundary staggering limits! >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> >> >> Any suggestions? What can I do to run it? >> >> Thanks >> Ula >> >>> Hi, >>> >>> Did you try to debug your setup by running a normal single-replica >>> simulation first? >>> >>> Mark >>> >>> On Fri, Jan 5, 2018 at 12:12 PM Urszula Uciechowska < >>> urszula.uciechow...@biotech.ug.edu.pl> wrote: >>> Dear gromacs users, I am trying to run REMD simulations using 4.5.5 version (implicit solvent). The MD procedure: pdb2gmx -f prot.pdb -o prot.gro -q prot.pdb -ignh -ss. The input for minimization step: ; Run control parameters integrator = cg nsteps = 800 vdwtype = cut-off coulombtype = cut-off ;cutoff-scheme= group pbc = no periodic_molecules = no nstlist = 10 ns_type = grid rlist= 1.0 rcoulomb = 1.6 rvdw = 1.6 comm-mode= Angular nstcomm = 10 ; ;Energy minimizing stuff ; emtol= 100.0 nstcgsteep = 2 emstep = 0.01 ; ;Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; ; Implicit solvent ; implicit_solvent = GBSA gb_algorithm = OBC ;Still HCT OBC nstgbradii = 1.0 rgbradii = 1.0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent gb_saltconc = 0; Salt concentration for implicit solvent models, currently not used sa_algorithm = Ace-approximation sa_surface_tension = 2.05016 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA. The value -1 will set default value for Still/HCT/OBC GB-models. and it finished without errors. The problem is with equilibration step. The input file that I used is: ; MD CONTROL OPTIONS integrator = md dt = 0.002 nsteps = 5 ; 10 ns init_step = 0; For exact run continuation or redoing part of a run comm-mode = Angular ; mode for center of mass motion removal nstcomm = 10 ; number of steps for center of mass motion removal ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency for energies to log file and energy file nstlog = 1000 nstcalcenergy= 10 nstenergy= 1000 ; Neighbor searching and Electrostatitcs vdwtype = cut-off coulombtype = cut-off ;cutoff-scheme= group pbc = no periodic_molecules = no nstlist = 5 ns_type = grid rlist= 1.0 rcoulomb = 1.6 rvdw = 1.0 ; Selection of energy groups energygrps = fixed not_fixed freezegrps = fixed not_fixed freezedim= Y Y Y N N N ;Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Temperutare coupling tcoupl = v-rescale tc_grps = fixed not_fixed tau_t= 0.01 0.01 ;nst_couple = 5 ref_t= 300.00 300.00 ; Pressure coupling pcoupl = no ;pcoupletype = isotropic tau_p= 1.0 ;compressiblity = 4.5e-5 ref_p= 1.0 gen_vel = yes gen_temp =
Re: [gmx-users] REMD DLB bug
Hi, The fix will be released in an upcoming 2016.5 patch release. (which you can see in the redmine issue page "Target version" field BTW). Cheers, -- Szilárd On Mon, Feb 12, 2018 at 2:49 PM, Akshay wrote: > Hello All, > > I was running REMD simulations on Gromacs 2016.1 when my simulation crashed > with the error > > Assertion failed: > Condition: comm->cycl_n[ddCyclStep] > 0 > When we turned on DLB, we should have measured cycles > > I saw that there was a bug #2298 reported about this recently at > https://redmine.gromacs.org/issues/2298. I wanted to know if this fix has > been implemented in the latest 2018 or 2016.4 versions? > > Thanks, > Akshay > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD - subsystems not compatible
Hi gmx-users, I am trying to start a replica exchange simulation of a model peptide in water, but can’t get it to run properly. I have limited experience with REMD, so I thought I’d ask here for all the rookie mistakes it is possible to do. I have also seen the earlier discussions about the error message, but those seemed to be related to restarts and/or continuations, rather than not being able to run at all. My gromacs version is 2016 (for compatibility reasons), and the exact error message I get is this: --- Program: gmx mdrun, version 2016.5 Source file: src/gromacs/mdlib/main.cpp (line 115) MPI rank:32 (out of 62) Fatal error: The 62 subsystems are not compatible I followed Marks tutorial on the gromacs website and have a small bash-script that loops over all desired temperatures, run equilibration etc. I then start the simulation like this: $MPIRUN $GMX mdrun $ntmpi -ntomp $ntomp -deffnm sim -replex 500 -multidir ~pfs/ferring/gnrh_aa/dipep_remd/sim* What could be the source of this incompatibility? Many thanks /Per -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD analysis of trajectories
Hi, I have run a 100ns-REMD of protein, which has 20 replicas (i.e. remd1.xtc, remd2.xtc, ..., remd20.xtc). I want to analyze a trajectory at specific temperature such as a trajectory at experiment temperature 298K rather than analyzing the continuous trajectory. I have known GROMACS exchange coordinate when REMD running. Do I just analyze remd2.xtc of replica 2(T=298K) if I want to analyze a trajectory at 298K? Do I need to do something else on the trajectories to get a trajectory at specific temperature(i.e. 298K)? Best regards, Ouyang -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD stall out
Hi, If I understand correctly your jobs stall, what is in the log output? What about the console? Does this happen without PLUMED? -- Szilárd On Tue, Feb 11, 2020 at 7:56 PM Daniel Burns wrote: > Hi, > > I continue to have trouble getting an REMD job to run. It never makes it > to the point that it generates trajectory files but it never gives any > error either. > > I have switched from a large TREMD with 72 replicas to the Plumed > Hamiltonian method with only 6 replicas. Everything is now on one node and > each replica has 6 cores. I've turned off the dynamic load balancing on > this attempt per the recommendation from the Plumed site. > > Any ideas on how to troubleshoot? > > Thank you, > > Dan > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD stall out
HI Szilard, I've deleted all my output but all the writing to the log and console stops around the step noting the domain decomposition (or other preliminary task). It is the same with or without Plumed - the TREMD with Gromacs only was the first thing to present this issue. I've discovered that if each replica is assigned its own node, the simulations proceed. If I try to run several replicas on each node (divided evenly), the simulations stall out before any trajectories get written. I have tried many different -np and -ntomp options as well as several slurm job submission scripts with node/ thread configurations but multiple simulations per node will not work. I need to be able to run several replicas on the same node to get enough data since it's hard to get more than 8 nodes (and as a result, replicas). Thanks for your reply. -Dan On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns wrote: > Hi, > > I continue to have trouble getting an REMD job to run. It never makes it > to the point that it generates trajectory files but it never gives any > error either. > > I have switched from a large TREMD with 72 replicas to the Plumed > Hamiltonian method with only 6 replicas. Everything is now on one node and > each replica has 6 cores. I've turned off the dynamic load balancing on > this attempt per the recommendation from the Plumed site. > > Any ideas on how to troubleshoot? > > Thank you, > > Dan > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD stall out
Hi Dan, What you describe in not an expected behaviro and it is something we should look into. What GROMACS version were you using? One thing that may help diagnosing the issue is: try to disable replica exchange and run -multidir that way. Does the simulation proceed? Can you please open an issue on redmine.gromacs.org and upload the necessary input files to reproduce, logs of your runs that reproduced the issue. Cheers, -- Szilárd On Mon, Feb 17, 2020 at 3:56 PM Daniel Burns wrote: > HI Szilard, > > I've deleted all my output but all the writing to the log and console stops > around the step noting the domain decomposition (or other preliminary > task). It is the same with or without Plumed - the TREMD with Gromacs only > was the first thing to present this issue. > > I've discovered that if each replica is assigned its own node, the > simulations proceed. If I try to run several replicas on each node > (divided evenly), the simulations stall out before any trajectories get > written. > > I have tried many different -np and -ntomp options as well as several slurm > job submission scripts with node/ thread configurations but multiple > simulations per node will not work. I need to be able to run several > replicas on the same node to get enough data since it's hard to get more > than 8 nodes (and as a result, replicas). > > Thanks for your reply. > > -Dan > > On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns wrote: > > > Hi, > > > > I continue to have trouble getting an REMD job to run. It never makes it > > to the point that it generates trajectory files but it never gives any > > error either. > > > > I have switched from a large TREMD with 72 replicas to the Plumed > > Hamiltonian method with only 6 replicas. Everything is now on one node > and > > each replica has 6 cores. I've turned off the dynamic load balancing on > > this attempt per the recommendation from the Plumed site. > > > > Any ideas on how to troubleshoot? > > > > Thank you, > > > > Dan > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD stall out
Hi, That could be caused by configuration of the parallel file system or MPI on your cluster. If only one file descriptor is available per node to an MPI job, then your symptoms are explained. Some kinds of compute jobs follow such a model, so maybe someone optimized something for that. Mark On Mon, 17 Feb 2020 at 15:56, Daniel Burns wrote: > HI Szilard, > > I've deleted all my output but all the writing to the log and console stops > around the step noting the domain decomposition (or other preliminary > task). It is the same with or without Plumed - the TREMD with Gromacs only > was the first thing to present this issue. > > I've discovered that if each replica is assigned its own node, the > simulations proceed. If I try to run several replicas on each node > (divided evenly), the simulations stall out before any trajectories get > written. > > I have tried many different -np and -ntomp options as well as several slurm > job submission scripts with node/ thread configurations but multiple > simulations per node will not work. I need to be able to run several > replicas on the same node to get enough data since it's hard to get more > than 8 nodes (and as a result, replicas). > > Thanks for your reply. > > -Dan > > On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns wrote: > > > Hi, > > > > I continue to have trouble getting an REMD job to run. It never makes it > > to the point that it generates trajectory files but it never gives any > > error either. > > > > I have switched from a large TREMD with 72 replicas to the Plumed > > Hamiltonian method with only 6 replicas. Everything is now on one node > and > > each replica has 6 cores. I've turned off the dynamic load balancing on > > this attempt per the recommendation from the Plumed site. > > > > Any ideas on how to troubleshoot? > > > > Thank you, > > > > Dan > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD stall out
Thanks Mark and Szilard, I forwarded Mark's suggestion to IT. I'll see what they have to say and then I'll try the simulation again and open an issue on redime. Thank you, Dan On Mon, Feb 17, 2020 at 9:09 AM Mark Abraham wrote: > Hi, > > That could be caused by configuration of the parallel file system or MPI on > your cluster. If only one file descriptor is available per node to an MPI > job, then your symptoms are explained. Some kinds of compute jobs follow > such a model, so maybe someone optimized something for that. > > Mark > > On Mon, 17 Feb 2020 at 15:56, Daniel Burns wrote: > > > HI Szilard, > > > > I've deleted all my output but all the writing to the log and console > stops > > around the step noting the domain decomposition (or other preliminary > > task). It is the same with or without Plumed - the TREMD with Gromacs > only > > was the first thing to present this issue. > > > > I've discovered that if each replica is assigned its own node, the > > simulations proceed. If I try to run several replicas on each node > > (divided evenly), the simulations stall out before any trajectories get > > written. > > > > I have tried many different -np and -ntomp options as well as several > slurm > > job submission scripts with node/ thread configurations but multiple > > simulations per node will not work. I need to be able to run several > > replicas on the same node to get enough data since it's hard to get more > > than 8 nodes (and as a result, replicas). > > > > Thanks for your reply. > > > > -Dan > > > > On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns > wrote: > > > > > Hi, > > > > > > I continue to have trouble getting an REMD job to run. It never makes > it > > > to the point that it generates trajectory files but it never gives any > > > error either. > > > > > > I have switched from a large TREMD with 72 replicas to the Plumed > > > Hamiltonian method with only 6 replicas. Everything is now on one node > > and > > > each replica has 6 cores. I've turned off the dynamic load balancing > on > > > this attempt per the recommendation from the Plumed site. > > > > > > Any ideas on how to troubleshoot? > > > > > > Thank you, > > > > > > Dan > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD stall out
Hi again, It seems including our openmp module was responsible for the issue the whole time. When I submit the job only loading pmix and gromacs, replica exchange proceeds. Thank you, Dan On Mon, Feb 17, 2020 at 9:09 AM Mark Abraham wrote: > Hi, > > That could be caused by configuration of the parallel file system or MPI on > your cluster. If only one file descriptor is available per node to an MPI > job, then your symptoms are explained. Some kinds of compute jobs follow > such a model, so maybe someone optimized something for that. > > Mark > > On Mon, 17 Feb 2020 at 15:56, Daniel Burns wrote: > > > HI Szilard, > > > > I've deleted all my output but all the writing to the log and console > stops > > around the step noting the domain decomposition (or other preliminary > > task). It is the same with or without Plumed - the TREMD with Gromacs > only > > was the first thing to present this issue. > > > > I've discovered that if each replica is assigned its own node, the > > simulations proceed. If I try to run several replicas on each node > > (divided evenly), the simulations stall out before any trajectories get > > written. > > > > I have tried many different -np and -ntomp options as well as several > slurm > > job submission scripts with node/ thread configurations but multiple > > simulations per node will not work. I need to be able to run several > > replicas on the same node to get enough data since it's hard to get more > > than 8 nodes (and as a result, replicas). > > > > Thanks for your reply. > > > > -Dan > > > > On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns > wrote: > > > > > Hi, > > > > > > I continue to have trouble getting an REMD job to run. It never makes > it > > > to the point that it generates trajectory files but it never gives any > > > error either. > > > > > > I have switched from a large TREMD with 72 replicas to the Plumed > > > Hamiltonian method with only 6 replicas. Everything is now on one node > > and > > > each replica has 6 cores. I've turned off the dynamic load balancing > on > > > this attempt per the recommendation from the Plumed site. > > > > > > Any ideas on how to troubleshoot? > > > > > > Thank you, > > > > > > Dan > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD stall out
This was not actually the solution. Wanted to follow up in case someone else is experiencing this problem. We are reinstalling the openmp version. On Thu, Feb 20, 2020 at 3:10 PM Daniel Burns wrote: > Hi again, > > It seems including our openmp module was responsible for the issue the > whole time. When I submit the job only loading pmix and gromacs, replica > exchange proceeds. > > Thank you, > > Dan > > On Mon, Feb 17, 2020 at 9:09 AM Mark Abraham > wrote: > >> Hi, >> >> That could be caused by configuration of the parallel file system or MPI >> on >> your cluster. If only one file descriptor is available per node to an MPI >> job, then your symptoms are explained. Some kinds of compute jobs follow >> such a model, so maybe someone optimized something for that. >> >> Mark >> >> On Mon, 17 Feb 2020 at 15:56, Daniel Burns wrote: >> >> > HI Szilard, >> > >> > I've deleted all my output but all the writing to the log and console >> stops >> > around the step noting the domain decomposition (or other preliminary >> > task). It is the same with or without Plumed - the TREMD with Gromacs >> only >> > was the first thing to present this issue. >> > >> > I've discovered that if each replica is assigned its own node, the >> > simulations proceed. If I try to run several replicas on each node >> > (divided evenly), the simulations stall out before any trajectories get >> > written. >> > >> > I have tried many different -np and -ntomp options as well as several >> slurm >> > job submission scripts with node/ thread configurations but multiple >> > simulations per node will not work. I need to be able to run several >> > replicas on the same node to get enough data since it's hard to get more >> > than 8 nodes (and as a result, replicas). >> > >> > Thanks for your reply. >> > >> > -Dan >> > >> > On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns >> wrote: >> > >> > > Hi, >> > > >> > > I continue to have trouble getting an REMD job to run. It never >> makes it >> > > to the point that it generates trajectory files but it never gives any >> > > error either. >> > > >> > > I have switched from a large TREMD with 72 replicas to the Plumed >> > > Hamiltonian method with only 6 replicas. Everything is now on one >> node >> > and >> > > each replica has 6 cores. I've turned off the dynamic load balancing >> on >> > > this attempt per the recommendation from the Plumed site. >> > > >> > > Any ideas on how to troubleshoot? >> > > >> > > Thank you, >> > > >> > > Dan >> > > >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to gmx-users-requ...@gromacs.org. >> > >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD on GPU
On Thu, Nov 28, 2013 at 3:01 PM, James Starlight wrote: > Dear Gromacs users! > > I'd like to perform replica exchange simulation > > For this I've made bash script which create n folders like > replica-298 > replica-312 > replica-323 > replica-334 > ... > replica-N > with all files needed for simulation considted of specified mdp file with > different ref_t value > No I'd like to launch this simulation using > -multidir replica-298 replica-312 replica-323 replica-334 > > Unfortunately I've obtained > > Fatal error: > mdrun -multi is not supported with the thread library.Please compile > GROMACS with MPI support > > Does it possible to install mpirun on the existing Gromacs-4.6 built from > source (without removing of the installed files)? > No, please compile GROMACS with MPI support, per the installation instructions. > Does it possible to run replica simulations in GPU supported mode ? > Yes, but you need to compile for both GPU and MPI. And see http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Using_multi-simulations_and_GPUs for mdrun tips. Mark Thanks for help, > > James > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD slow's down drastically
Dear members, I am trying to run REMD simulation for poly Alanine (12 residue) system. I used remd generator to get the range of temperature with the exchange probability of 0.3. I was getting the 125 replicas. I tried to simulate 125 replicas its drastically slow down the simulation time (for 70 pico seconds it took around 17 hours ) could anyone please tell me how to solve this issue. Following is the MDP file title = G4Ga3a4a5 production. ;define = ;-DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 1250 ; 2 * 500 = 3ns dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; save coordinates every 0.2 ps nstvout = 1 ; save velocities every 0.2 ps nstxtcout = 500 ; save xtc coordinate every 0.2 ps nstenergy = 500 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = yes ; Restarting after NVT constraint_algorithm = lincs ; holonomic constraints constraints = hbonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy morse = no ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = protein SOL Cl ;two coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = X X X ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme regards singam -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD Melting Curve
On 2014-03-04 00:20, atanu_das wrote: Dear Gromacs users, I have performed a REMD simulation with 12 replicas exponentially spaced between 260-420K. However, when I applied g_kinetics program to generate the melting curve, I got 161 values starting from 260K to 420K having the folded fraction reported at each temperature. My question is if I am applying 12 replicas exponentially spaced in the temperature range chosen, how could I get 161 values? Am I doing something wrong? Does g_kinetics in GROMACS use any smoothing function to generate the intermediate temperature and folded fraction values? Please suggest/advise. Atanu What kind of values? You get one fraction folded per replica, right? Did you succesfully run the demux.pl? -- View this message in context: http://gromacs.5086.x6.nabble.com/REMD-Melting-Curve-tp5014920.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD Melting Curve
Dear Sir, I successfully ran demix.pl and generated the xvg files - replica_ndx.xvg and replica_temp.xvg. I am attaching the file that I got as melt.xvg below .. # This file was created Wed Feb 26 10:10:27 2014 # by the following command: # g_kinetics_d -f replica_temp.xvg -d replica_index.xvg # # g_kinetics_d is part of G R O M A C S: # # Groningen Machine for Chemical Simulation # @ title "Melting curve" @ xaxis label "T (K)" @ yaxis label "" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Folded fraction" @ s1 legend "DG (kJ/mole)" 260 0.929 5.556 261 0.927 5.500 262 0.924 5.445 263 0.922 5.389 264 0.919 5.334 265 0.916 5.278 266 0.914 5.223 267 0.911 5.167 268 0.908 5.112 269 0.906 5.056 270 0.903 5.000 271 0.900 4.945 272 0.897 4.889 273 0.894 4.834 274 0.891 4.778 275 0.888 4.723 276 0.884 4.667 277 0.881 4.612 278 0.878 4.556 279 0.874 4.500 280 0.871 4.445 281 0.867 4.389 282 0.864 4.334 283 0.860 4.278 284 0.857 4.223 285 0.853 4.167 286 0.849 4.112 287 0.845 4.056 288 0.842 4.000 289 0.838 3.945 290 0.834 3.889 291 0.830 3.834 292 0.826 3.778 293 0.822 3.723 294 0.818 3.667 295 0.813 3.612 296 0.809 3.556 297 0.805 3.500 298 0.801 3.445 299 0.796 3.389 300 0.792 3.334 301 0.787 3.278 302 0.783 3.223 303 0.779 3.167 304 0.774 3.112 305 0.769 3.056 306 0.765 3.000 307 0.760 2.945 308 0.756 2.889 309 0.751 2.834 310 0.746 2.778 311 0.741 2.723 312 0.737 2.667 313 0.732 2.612 314 0.727 2.556 315 0.722 2.500 316 0.717 2.445 317 0.712 2.389 318 0.707 2.334 319 0.702 2.278 320 0.697 2.223 321 0.693 2.167 322 0.688 2.112 323 0.683 2.056 324 0.678 2.001 325 0.673 1.945 326 0.668 1.889 327 0.663 1.834 328 0.657 1.778 329 0.652 1.723 330 0.647 1.667 331 0.642 1.612 332 0.637 1.556 333 0.632 1.501 334 0.627 1.445 335 0.622 1.389 336 0.617 1.334 337 0.612 1.278 338 0.607 1.223 339 0.602 1.167 340 0.597 1.112 341 0.592 1.056 342 0.587 1.001 343 0.582 0.945 344 0.577 0.889 345 0.572 0.834 346 0.567 0.778 347 0.562 0.723 348 0.557 0.667 349 0.553 0.612 350 0.548 0.556 351 0.543 0.501 352 0.538 0.445 353 0.533 0.389 354 0.528 0.334 355 0.524 0.278 356 0.519 0.223 357 0.514 0.167 358 0.509 0.112 359 0.505 0.056 360 0.500 0.001 361 0.495 -0.055 362 0.491 -0.111 363 0.486 -0.166 364 0.482 -0.222 365 0.477 -0.277 366 0.473 -0.333 367 0.468 -0.388 368 0.464 -0.444 369 0.459 -0.499 370 0.455 -0.555 371 0.451 -0.611 372 0.446 -0.666 373 0.442 -0.722 374 0.438 -0.777 375 0.434 -0.833 376 0.429 -0.888 377 0.425 -0.944 378 0.421 -0.999 379 0.417 -1.055 380 0.413 -1.111 381 0.409 -1.166 382 0.405 -1.222 383 0.401 -1.277 384 0.397 -1.333 385 0.393 -1.388 386 0.389 -1.444 387 0.386 -1.499 388 0.382 -1.555 389 0.378 -1.610 390 0.374 -1.666 391 0.371 -1.722 392 0.367 -1.777 393 0.363 -1.833 394 0.360 -1.888 395 0.356 -1.944 396 0.353 -1.999 397 0.349 -2.055 398 0.346 -2.110 399 0.342 -2.166 400 0.339 -2.222 401 0.336 -2.277 402 0.332 -2.333 403 0.329 -2.388 404 0.326 -2.444 405 0.323 -2.499 406 0.319 -2.555 407 0.316 -2.610 408 0.313 -2.666 409 0.310 -2.722 410 0.307 -2.777 411 0.304 -2.833 412 0.301 -2.888 413 0.298 -2.944 414 0.295 -2.999 415 0.292 -3.055 416 0.289 -3.110 417 0.286 -3.166 418 0.284 -3.222 419 0.281 -3.277 420 0.278 -3.333 So, as you can see, I got folded fraction and associated free energy change at each temperature ranging from 260-420K. Atanu On Tuesday, 4 Mar
Re: [gmx-users] REMD Melting Curve
On 3/4/14, 12:22 PM, atanu das wrote: Dear Sir, I successfully ran demix.pl and generated the xvg files - replica_ndx.xvg and replica_temp.xvg. I am attaching the file that I got as melt.xvg below .. # This file was created Wed Feb 26 10:10:27 2014 # by the following command: # g_kinetics_d -f replica_temp.xvg -d replica_index.xvg # # g_kinetics_d is part of G R O M A C S: # # Groningen Machine for Chemical Simulation # @title "Melting curve" @xaxis label "T (K)" @yaxis label "" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Folded fraction" @ s1 legend "DG (kJ/mole)" 260 0.929 5.556 261 0.927 5.500 262 0.924 5.445 263 0.922 5.389 264 0.919 5.334 265 0.916 5.278 266 0.914 5.223 267 0.911 5.167 268 0.908 5.112 269 0.906 5.056 270 0.903 5.000 271 0.900 4.945 272 0.897 4.889 273 0.894 4.834 274 0.891 4.778 275 0.888 4.723 276 0.884 4.667 277 0.881 4.612 278 0.878 4.556 279 0.874 4.500 280 0.871 4.445 281 0.867 4.389 282 0.864 4.334 283 0.860 4.278 284 0.857 4.223 285 0.853 4.167 286 0.849 4.112 287 0.845 4.056 288 0.842 4.000 289 0.838 3.945 290 0.834 3.889 291 0.830 3.834 292 0.826 3.778 293 0.822 3.723 294 0.818 3.667 295 0.813 3.612 296 0.809 3.556 297 0.805 3.500 298 0.801 3.445 299 0.796 3.389 300 0.792 3.334 301 0.787 3.278 302 0.783 3.223 303 0.779 3.167 304 0.774 3.112 305 0.769 3.056 306 0.765 3.000 307 0.760 2.945 308 0.756 2.889 309 0.751 2.834 310 0.746 2.778 311 0.741 2.723 312 0.737 2.667 313 0.732 2.612 314 0.727 2.556 315 0.722 2.500 316 0.717 2.445 317 0.712 2.389 318 0.707 2.334 319 0.702 2.278 320 0.697 2.223 321 0.693 2.167 322 0.688 2.112 323 0.683 2.056 324 0.678 2.001 325 0.673 1.945 326 0.668 1.889 327 0.663 1.834 328 0.657 1.778 329 0.652 1.723 330 0.647 1.667 331 0.642 1.612 332 0.637 1.556 333 0.632 1.501 334 0.627 1.445 335 0.622 1.389 336 0.617 1.334 337 0.612 1.278 338 0.607 1.223 339 0.602 1.167 340 0.597 1.112 341 0.592 1.056 342 0.587 1.001 343 0.582 0.945 344 0.577 0.889 345 0.572 0.834 346 0.567 0.778 347 0.562 0.723 348 0.557 0.667 349 0.553 0.612 350 0.548 0.556 351 0.543 0.501 352 0.538 0.445 353 0.533 0.389 354 0.528 0.334 355 0.524 0.278 356 0.519 0.223 357 0.514 0.167 358 0.509 0.112 359 0.505 0.056 360 0.500 0.001 361 0.495-0.055 362 0.491-0.111 363 0.486-0.166 364 0.482-0.222 365 0.477-0.277 366 0.473-0.333 367 0.468-0.388 368 0.464-0.444 369 0.459-0.499 370 0.455-0.555 371 0.451-0.611 372 0.446-0.666 373 0.442-0.722 374 0.438-0.777 375 0.434-0.833 376 0.429-0.888 377 0.425-0.944 378 0.421-0.999 379 0.417-1.055 380 0.413-1.111 381 0.409-1.166 382 0.405-1.222 383 0.401-1.277 384 0.397-1.333 385 0.393-1.388 386 0.389-1.444 387 0.386-1.499 388 0.382-1.555 389 0.378-1.610 390 0.374-1.666 391 0.371-1.722 392 0.367-1.777 393 0.363-1.833 394 0.360-1.888 395 0.356-1.944 396 0.353-1.999 397 0.349-2.055 398 0.346-2.110 399 0.342-2.166 400 0.339-2.222 401 0.336-2.277 402 0.332-2.333 403 0.329-2.388 404 0.326-2.444 405 0.323-2.499 406 0.319-2.555 407 0.316-2.610 408 0.313-2.666 409 0.310-2.722 410 0.307-2.777 411 0.304-2.833 412 0.301-2.888 413 0.298-2.944 414 0.295-2.999 415 0.292-3.055 416 0.289-3.110 417 0.286-3.166 418 0.284-3.22
Re: [gmx-users] REMD Melting Curve
Thanks Justin. That's reassuring. However, I was wondering if any smoothing function is used in getting the melted fractions at intermediate temperatures with 1-K resolution. I could not find it in the description of the g_kinetics program. I need to know this because - (1) to justify my result to a person who would ask how I am getting values more than the number of replicas being used and (2) if I know the smoothing function then I would be able to estimate the temperature when folded fraction f=0. Because then I would be able to extract the free energy of complete unfolding as currently the melted fraction stops as 0.278. -Atanu On Tuesday, 4 March 2014 4:01 PM, Justin Lemkul wrote: On 3/4/14, 12:22 PM, atanu das wrote: > Dear Sir, > I successfully ran demix.pl and generated the xvg files - >replica_ndx.xvg and replica_temp.xvg. I am attaching the file that I got as >melt.xvg below .. > > # This file was created Wed Feb 26 10:10:27 2014 > # by the following command: > # g_kinetics_d -f replica_temp.xvg -d replica_index.xvg > # > # g_kinetics_d is part of G R O M A C S: > # > # Groningen Machine for Chemical Simulation > # > @ title "Melting curve" > @ xaxis label "T (K)" > @ yaxis label "" > @TYPE xy > @ view 0.15, 0.15, 0.75, 0.85 > @ legend on > @ legend box on > @ legend loctype view > @ legend 0.78, 0.8 > @ legend length 2 > @ s0 legend "Folded fraction" > @ s1 legend "DG (kJ/mole)" > 260 0.929 5.556 > 261 0.927 5.500 > 262 0.924 5.445 > 263 0.922 5.389 > 264 0.919 5.334 > 265 0.916 5.278 > 266 0.914 5.223 > 267 0.911 5.167 > 268 0.908 5.112 > 269 0.906 5.056 > 270 0.903 5.000 > 271 0.900 4.945 > 272 0.897 4.889 > 273 0.894 4.834 > 274 0.891 4.778 > 275 0.888 4.723 > 276 0.884 4.667 > 277 0.881 4.612 > 278 0.878 4.556 > 279 0.874 4.500 > 280 0.871 4.445 > 281 0.867 4.389 > 282 0.864 4.334 > 283 0.860 4.278 > 284 0.857 4.223 > 285 0.853 4.167 > 286 0.849 4.112 > 287 0.845 4.056 > 288 0.842 4.000 > 289 0.838 3.945 > 290 0.834 3.889 > 291 0.830 3.834 > 292 0.826 3.778 > 293 0.822 3.723 > 294 0.818 3.667 > 295 0.813 3.612 > 296 0.809 3.556 > 297 0.805 3.500 > 298 0.801 3.445 > 299 0.796 3.389 > 300 0.792 3.334 > 301 0.787 3.278 > 302 0.783 3.223 > 303 0.779 3.167 > 304 0.774 3.112 > 305 0.769 3.056 > 306 0.765 3.000 > 307 0.760 2.945 > 308 0.756 2.889 > 309 0.751 2.834 > 310 0.746 2.778 > 311 0.741 2.723 > 312 0.737 2.667 > 313 0.732 2.612 > 314 0.727 2.556 > 315 0.722 2.500 > 316 0.717 2.445 > 317 0.712 2.389 > 318 0.707 2.334 > 319 0.702 2.278 > 320 0.697 2.223 > 321 0.693 2.167 > 322 0.688 2.112 > 323 0.683 2.056 > 324 0.678 2.001 > 325 0.673 1.945 > 326 0.668 1.889 > 327 0.663 1.834 > 328 0.657 1.778 > 329 0.652 1.723 > 330 0.647 1.667 > 331 0.642 1.612 > 332 0.637 1.556 > 333 0.632 1.501 > 334 0.627 1.445 > 335 0.622 1.389 > 336 0.617 1.334 > 337 0.612 1.278 > 338 0.607 1.223 > 339 0.602 1.167 > 340 0.597 1.112 > 341 0.592 1.056 > 342 0.587 1.001 > 343 0.582 0.945 > 344 0.577 0.889 > 345 0.572 0.834 > 346 0.567 0.778 > 347 0.562 0.723 > 348 0.557 0.667 > 349 0.553 0.612 > 350 0.548 0.556 > 351 0.543 0.501 > 352 0.538 0.445 > 353 0.533 0.389 > 354 0.528 0.334 > 355 0.524 0.278 > 356 0.519 0.223 > 357 0.514 0.167 > 358 0.509 0.112 > 359 0.505 0.056 > 360 0.500 0.001 > 361 0.495 -0.055 > 362 0.491 -0.111 > 363 0.486 -0.166 > 364 0.482 -0.222 > 365 0.477 -0.277 > 366 0.473 -0.333 > 367 0.468 -0.388 > 368 0.464 -0.444 > 369 0.459 -0.499 > 370 0.455 -0.555 > 371 0.451 -0.611 > 372 0.446 -0.666 > 373 0.442 -0.722 > 374 0.438 -0.777 > 375 0.434 -0.833 > 376 0.429 -0.888 > 377 0.425 -0.944 > 378 0.421 -0.999 > 379 0.417 -1.055 > 380 0.413 -1.111 > 381 0.409
Re: [gmx-users] REMD Melting Curve
On 3/4/14, 11:26 PM, atanu das wrote: Thanks Justin. That's reassuring. However, I was wondering if any smoothing function is used in getting the melted fractions at intermediate temperatures with 1-K resolution. I could not find it in the description of the g_kinetics program. I need to know this because - (1) to justify my result to a person who would ask how I am getting values more than the number of replicas being used and (2) if I know the smoothing function then I would be able to estimate the temperature when folded fraction f=0. Because then I would be able to extract the free energy of complete unfolding as currently the melted fraction stops as 0.278. -Atanu There are no smoothing functions applied in the melting curve. It is a very simple calculation relating probability to free energy. It should be very easy to expand the code to create a profile over a greater temperature range, and even make these command-line options for greater flexibility. -Justin On Tuesday, 4 March 2014 4:01 PM, Justin Lemkul wrote: On 3/4/14, 12:22 PM, atanu das wrote: Dear Sir, I successfully ran demix.pl and generated the xvg files - replica_ndx.xvg and replica_temp.xvg. I am attaching the file that I got as melt.xvg below .. # This file was created Wed Feb 26 10:10:27 2014 # by the following command: # g_kinetics_d -f replica_temp.xvg -d replica_index.xvg # # g_kinetics_d is part of G R O M A C S: # # Groningen Machine for Chemical Simulation # @title "Melting curve" @xaxis label "T (K)" @ yaxis label "" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Folded fraction" @ s1 legend "DG (kJ/mole)" 260 0.929 5.556 261 0.927 5.500 262 0.924 5.445 263 0.922 5.389 264 0.919 5.334 265 0.916 5.278 266 0.914 5.223 267 0.911 5.167 268 0.908 5.112 269 0.906 5.056 270 0.903 5.000 271 0.900 4.945 272 0.897 4.889 273 0.894 4.834 274 0.891 4.778 275 0.888 4.723 276 0.884 4.667 277 0.881 4.612 278 0.878 4.556 279 0.874 4.500 280 0.871 4.445 281 0.867 4.389 282 0.864 4.334 283 0.860 4.278 284 0.857 4.223 285 0.853 4.167 286 0.849 4.112 287 0.845 4.056 288 0.842 4.000 289 0.838 3.945 290 0.834 3.889 291 0.830 3.834 292 0.826 3.778 293 0.822 3.723 294 0.818 3.667 295 0.813 3.612 296 0.809 3.556 297 0.805 3.500 298 0.801 3.445 299 0.796 3.389 300 0.792 3.334 301 0.787 3.278 302 0.783 3.223 303 0.779 3.167 304 0.774 3.112 305 0.769 3.056 306 0.765 3.000 307 0.760 2.945 308 0.756 2.889 309 0.751 2.834 310 0.746 2.778 311 0.741 2.723 312 0.737 2.667 313 0.732 2.612 314 0.727 2.556 315 0.722 2.500 316 0.717 2.445 317 0.712 2.389 318 0.707 2.334 319 0.702 2.278 320 0.697 2.223 321 0.693 2.167 322 0.688 2.112 323 0.683 2.056 324 0.678 2.001 325 0.673 1.945 326 0.668 1.889 327 0.663 1.834 328 0.657 1.778 329 0.652 1.723 330 0.647 1.667 331 0.642 1.612 332 0.637 1.556 333 0.632 1.501 334 0.627 1.445 335 0.622 1.389 336 0.617 1.334 337 0.612 1.278 338 0.607 1.223 339 0.602 1.167 340 0.597 1.112 341 0.592 1.056 342 0.587 1.001 343 0.582 0.945 344 0.577 0.889 345 0.572 0.834 346 0.567 0.778 347 0.562 0.723 348 0.557 0.667 349 0.553 0.612 350 0.548 0.556 351 0.543 0.501 352 0.538 0.445 353 0.533 0.389 354 0.528 0.334 355 0.524 0.278 356 0.519 0.223 357 0.514 0.167 358 0.509 0.112 359 0.505 0.056 360 0.500 0.001 361 0.495-0.055 362 0.491-0.111 363 0.486 -0.166 364 0.482-0.222 365 0.477-0.277 366 0.473-0.333 367 0.468-0.388 368 0.464-0.444 369 0.459-0.499 370 0.455-0.555 371 0.451-0.611 372 0.446-0.666 373 0.442-0.722 374 0.438-0.777 375 0.434-0.833 376 0.429-0.888 377 0.425-0.944 378 0.421-0.999 379 0.417-1.055 380 0.413-1.111 381 0.409-1.166 382 0.405-1.222 383 0.401-1.277 384 0.397-1.333 385 0.393-1.388 386 0.389-1.444 387 0.386-1.499 388 0.382-1.555 389 0.378-1.610 390 0.374-1.666 391 0.371-1.722 392 0.367-1.777 393 0.363-1.833 394 0.360-1.888 395 0.356-1.944 396 0.353-1.999 397 0.349-2.055 398 0.346-2.110 399 0.342-2.166 400 0.339 -2.222 401 0.336-2.277
Re: [gmx-users] REMD ensemble of states
Hi, Mdrun wrote that. You made the trajectories contiguous with the demux. Mark On Tue, 8 Nov 2016 04:55 Abramyan, Tigran wrote: > Hi, > > > I conducted REMD, and extracted the trajectories via > trjcat -f *.trr -demux replica_index.xvg > And now I was wondering which *.xtc file is the ensemble of states at the > baseline replica (lowest temperature replica). Intuitively my guess is that > the numbers in the names of *_trajout.xtc files correspond to the replica > numbers starting from the baseline, and hence 0_trajout.xtc is the ensemble > of states at the baseline replica, but I may be wrong. > > > Please suggest. > > > Thank you, > > Tigran > > > -- > Tigran M. Abramyan, Ph.D. > Postdoctoral Fellow, Computational Biophysics & Molecular Design > Center for Integrative Chemical Biology and Drug Discovery > Eshelman School of Pharmacy > University of North Carolina at Chapel Hill > Chapel Hill, NC 27599-7363 > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD ensemble of states
Hi Mark, Thanks a lot for your prompt response. So demux.pl creates continuous trajectories, *_trajout.xtc, but the ensemble of states (lowest energy ensemble, typically of interest in the analysis of REMD results) is saved in the original 0.xtc file produced during REMD before using demux.pl? Thank you, Tigran From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Tuesday, November 8, 2016 5:53 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] REMD ensemble of states Hi, Mdrun wrote that. You made the trajectories contiguous with the demux. Mark On Tue, 8 Nov 2016 04:55 Abramyan, Tigran wrote: > Hi, > > > I conducted REMD, and extracted the trajectories via > trjcat -f *.trr -demux replica_index.xvg > And now I was wondering which *.xtc file is the ensemble of states at the > baseline replica (lowest temperature replica). Intuitively my guess is that > the numbers in the names of *_trajout.xtc files correspond to the replica > numbers starting from the baseline, and hence 0_trajout.xtc is the ensemble > of states at the baseline replica, but I may be wrong. > > > Please suggest. > > > Thank you, > > Tigran > > > -- > Tigran M. Abramyan, Ph.D. > Postdoctoral Fellow, Computational Biophysics & Molecular Design > Center for Integrative Chemical Biology and Drug Discovery > Eshelman School of Pharmacy > University of North Carolina at Chapel Hill > Chapel Hill, NC 27599-7363 > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD ensemble of states
Yes On Tue, 8 Nov 2016 18:43 Abramyan, Tigran wrote: > Hi Mark, > > Thanks a lot for your prompt response. So demux.pl creates continuous > trajectories, *_trajout.xtc, but the ensemble of states (lowest energy > ensemble, typically of interest in the analysis of REMD results) is saved > in the original 0.xtc file produced during REMD before using demux.pl? > > Thank you, > Tigran > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark > Abraham > Sent: Tuesday, November 8, 2016 5:53 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] REMD ensemble of states > > Hi, > > Mdrun wrote that. You made the trajectories contiguous with the demux. > > Mark > > On Tue, 8 Nov 2016 04:55 Abramyan, Tigran wrote: > > > Hi, > > > > > > I conducted REMD, and extracted the trajectories via > > trjcat -f *.trr -demux replica_index.xvg > > And now I was wondering which *.xtc file is the ensemble of states at the > > baseline replica (lowest temperature replica). Intuitively my guess is > that > > the numbers in the names of *_trajout.xtc files correspond to the replica > > numbers starting from the baseline, and hence 0_trajout.xtc is the > ensemble > > of states at the baseline replica, but I may be wrong. > > > > > > Please suggest. > > > > > > Thank you, > > > > Tigran > > > > > > -- > > Tigran M. Abramyan, Ph.D. > > Postdoctoral Fellow, Computational Biophysics & Molecular Design > > Center for Integrative Chemical Biology and Drug Discovery > > Eshelman School of Pharmacy > > University of North Carolina at Chapel Hill > > Chapel Hill, NC 27599-7363 > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD ensemble of states
Thank you Mark, One more question regarding the centering of the frames at 300 replica (0.xtc) using trjconv. I have used a few trjconv options, however do not seem to be removing jumps from the original trajectory. For example, the command below works for me when applied to the *xtc file produced in regular MD, however, with REMD it produces a trajectory which won't be of use for example in VMD: echo 1 | trjconv -s 0.tpr -f 0.xtc -o 300.xtc -pbc nojump -dt 40 I am assuming I may need to use a combination of tpr files to produce the nojump 300.xtc file? Please advise, Thank you very much. Tigran From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Tuesday, November 8, 2016 1:15 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] REMD ensemble of states Yes On Tue, 8 Nov 2016 18:43 Abramyan, Tigran wrote: > Hi Mark, > > Thanks a lot for your prompt response. So demux.pl creates continuous > trajectories, *_trajout.xtc, but the ensemble of states (lowest energy > ensemble, typically of interest in the analysis of REMD results) is saved > in the original 0.xtc file produced during REMD before using demux.pl? > > Thank you, > Tigran > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark > Abraham > Sent: Tuesday, November 8, 2016 5:53 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] REMD ensemble of states > > Hi, > > Mdrun wrote that. You made the trajectories contiguous with the demux. > > Mark > > On Tue, 8 Nov 2016 04:55 Abramyan, Tigran wrote: > > > Hi, > > > > > > I conducted REMD, and extracted the trajectories via > > trjcat -f *.trr -demux replica_index.xvg > > And now I was wondering which *.xtc file is the ensemble of states at the > > baseline replica (lowest temperature replica). Intuitively my guess is > that > > the numbers in the names of *_trajout.xtc files correspond to the replica > > numbers starting from the baseline, and hence 0_trajout.xtc is the > ensemble > > of states at the baseline replica, but I may be wrong. > > > > > > Please suggest. > > > > > > Thank you, > > > > Tigran > > > > > > -- > > Tigran M. Abramyan, Ph.D. > > Postdoctoral Fellow, Computational Biophysics & Molecular Design > > Center for Integrative Chemical Biology and Drug Discovery > > Eshelman School of Pharmacy > > University of North Carolina at Chapel Hill > > Chapel Hill, NC 27599-7363 > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD ensemble of states
Hi, The ensemble at each temperature is intrinsically discontinuous. You can't make it look continuous. What are you trying to do? Mark On Mon, 14 Nov 2016 05:26 Abramyan, Tigran wrote: > Thank you Mark, > > One more question regarding the centering of the frames at 300 replica > (0.xtc) using trjconv. I have used a few trjconv options, however do not > seem to be removing jumps from the original trajectory. For example, the > command below works for me when applied to the *xtc file produced in > regular MD, however, with REMD it produces a trajectory which won't be of > use for example in VMD: > > echo 1 | trjconv -s 0.tpr -f 0.xtc -o 300.xtc -pbc nojump -dt 40 > > I am assuming I may need to use a combination of tpr files to produce the > nojump 300.xtc file? > > Please advise, > Thank you very much. > Tigran > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark > Abraham > Sent: Tuesday, November 8, 2016 1:15 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] REMD ensemble of states > > Yes > > On Tue, 8 Nov 2016 18:43 Abramyan, Tigran wrote: > > > Hi Mark, > > > > Thanks a lot for your prompt response. So demux.pl creates continuous > > trajectories, *_trajout.xtc, but the ensemble of states (lowest energy > > ensemble, typically of interest in the analysis of REMD results) is saved > > in the original 0.xtc file produced during REMD before using demux.pl? > > > > Thank you, > > Tigran > > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark > > Abraham > > Sent: Tuesday, November 8, 2016 5:53 AM > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] REMD ensemble of states > > > > Hi, > > > > Mdrun wrote that. You made the trajectories contiguous with the demux. > > > > Mark > > > > On Tue, 8 Nov 2016 04:55 Abramyan, Tigran wrote: > > > > > Hi, > > > > > > > > > I conducted REMD, and extracted the trajectories via > > > trjcat -f *.trr -demux replica_index.xvg > > > And now I was wondering which *.xtc file is the ensemble of states at > the > > > baseline replica (lowest temperature replica). Intuitively my guess is > > that > > > the numbers in the names of *_trajout.xtc files correspond to the > replica > > > numbers starting from the baseline, and hence 0_trajout.xtc is the > > ensemble > > > of states at the baseline replica, but I may be wrong. > > > > > > > > > Please suggest. > > > > > > > > > Thank you, > > > > > > Tigran > > > > > > > > > -- > > > Tigran M. Abramyan, Ph.D. > > > Postdoctoral Fellow, Computational Biophysics & Molecular Design > > > Center for Integrative Chemical Biology and Drug Discovery > > > Eshelman School of Pharmacy > > > University of North Carolina at Chapel Hill > > > Chapel Hill, NC 27599-7363 > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ.
Re: [gmx-users] REMD ensemble of states
Hi Mark, I understand that at each replica the coordinates of the accepted states are saved. I understand that I can calculate different properties of 0.xtc in differenr programs, e.g., gromacs, MDTraj, etc., but when it comes down to visualization in VMD, for example, in gromacs I don't seem to find a way to remove the jumps and superpose the coordinates saved in 0.xtc. Tigran From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Monday, November 14, 2016 1:20 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] REMD ensemble of states Hi, The ensemble at each temperature is intrinsically discontinuous. You can't make it look continuous. What are you trying to do? Mark On Mon, 14 Nov 2016 05:26 Abramyan, Tigran wrote: > Thank you Mark, > > One more question regarding the centering of the frames at 300 replica > (0.xtc) using trjconv. I have used a few trjconv options, however do not > seem to be removing jumps from the original trajectory. For example, the > command below works for me when applied to the *xtc file produced in > regular MD, however, with REMD it produces a trajectory which won't be of > use for example in VMD: > > echo 1 | trjconv -s 0.tpr -f 0.xtc -o 300.xtc -pbc nojump -dt 40 > > I am assuming I may need to use a combination of tpr files to produce the > nojump 300.xtc file? > > Please advise, > Thank you very much. > Tigran > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark > Abraham > Sent: Tuesday, November 8, 2016 1:15 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] REMD ensemble of states > > Yes > > On Tue, 8 Nov 2016 18:43 Abramyan, Tigran wrote: > > > Hi Mark, > > > > Thanks a lot for your prompt response. So demux.pl creates continuous > > trajectories, *_trajout.xtc, but the ensemble of states (lowest energy > > ensemble, typically of interest in the analysis of REMD results) is saved > > in the original 0.xtc file produced during REMD before using demux.pl? > > > > Thank you, > > Tigran > > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark > > Abraham > > Sent: Tuesday, November 8, 2016 5:53 AM > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] REMD ensemble of states > > > > Hi, > > > > Mdrun wrote that. You made the trajectories contiguous with the demux. > > > > Mark > > > > On Tue, 8 Nov 2016 04:55 Abramyan, Tigran wrote: > > > > > Hi, > > > > > > > > > I conducted REMD, and extracted the trajectories via > > > trjcat -f *.trr -demux replica_index.xvg > > > And now I was wondering which *.xtc file is the ensemble of states at > the > > > baseline replica (lowest temperature replica). Intuitively my guess is > > that > > > the numbers in the names of *_trajout.xtc files correspond to the > replica > > > numbers starting from the baseline, and hence 0_trajout.xtc is the > > ensemble > > > of states at the baseline replica, but I may be wrong. > > > > > > > > > Please suggest. > > > > > > > > > Thank you, > > > > > > Tigran > > > > > > > > > -- > > > Tigran M. Abramyan, Ph.D. > > > Postdoctoral Fellow, Computational Biophysics & Molecular Design > > > Center for Integrative Chemical Biology and Drug Discovery > > > Eshelman School of Pharmacy > > > University of North Carolina at Chapel Hill > > > Chapel Hill, NC 27599-7363 > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > &
[gmx-users] REMD Showing Zero Exchange Probability
Dear all, I have performed REMD for a system containing Protein, Reline, Urea and Water in the temperature range 290 to 450 K consist of 16 replicas out of 47 replicas generated by REMD temperature generator. But after the MD simulation the exchange probability is zero. I have used position restraints for reline, urea and protein. Is there any chance that position restraints cause the exchange probability to be zero? I have one more query that, the REMD temperature generator produced around 45 to 54 replicas for my system in the required temperature range. But I have only 80 processors to do the job, So is it necessary to choose the consecutive temperature replicas given by the REMD temperature generator or I can skip some temperatures in between? If I am using the equation *Ti = T0 exp (k* i)*, what determines the value of 'k' how it affects the exchange probability? How can I choose the value of 'k' for an arbitrary system? Thanks in advance... -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD and MARTINI force field
Hello, i would be interested in trying Replica exchange MD using a coarse grained representation of my system (MARTINI force field). I followed the tutorial of REMD with gromacs and all seemed to be fine ... However, running REMD at 300K 350K and 400K on my system in a first attempt, led to no exchange between replica with classical kT values approaching 1000 ! Repl 1 <-> 2 dE_term = 9.440e+02 (kT) Repl 1 <-> 2 dE_term = 9.945e+02 (kT) Repl 1 <-> 2 dE_term = 9.787e+02 (kT) Repl 1 <-> 2 dE_term = 1.006e+03 (kT) Repl 1 <-> 2 dE_term = 1.034e+03 (kT) Repl 1 <-> 2 dE_term = 9.542e+02 (kT) Repl 1 <-> 2 dE_term = 9.121e+02 (kT) Repl 1 <-> 2 dE_term = 9.453e+02 (kT) Any idea to help me ??? thank you in advance . Nicolas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD - subsystems not compatible
Hi, Generally the REMD code has written some analysis to the log file above this error message that should provide context. More generally, you can use gmx check to compare the .tpr files and observe that the differences between them are only what you expect. Mark On Wed, 24 Apr 2019 at 15:28, Per Larsson wrote: > Hi gmx-users, > > I am trying to start a replica exchange simulation of a model peptide in > water, but can’t get it to run properly. > I have limited experience with REMD, so I thought I’d ask here for all the > rookie mistakes it is possible to do. > I have also seen the earlier discussions about the error message, but > those seemed to be related to restarts and/or continuations, rather than > not being able to run at all. > > My gromacs version is 2016 (for compatibility reasons), and the exact > error message I get is this: > > --- > Program: gmx mdrun, version 2016.5 > Source file: src/gromacs/mdlib/main.cpp (line 115) > MPI rank:32 (out of 62) > > Fatal error: > The 62 subsystems are not compatible > > I followed Marks tutorial on the gromacs website and have a small > bash-script that loops over all desired temperatures, run equilibration > etc. > I then start the simulation like this: > > $MPIRUN $GMX mdrun $ntmpi -ntomp $ntomp -deffnm sim -replex 500 -multidir > ~pfs/ferring/gnrh_aa/dipep_remd/sim* > > What could be the source of this incompatibility? > > Many thanks > /Per > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD - subsystems not compatible
Thanks Mark for reminding me about the existence of the log files. Problem solved, the difference is clearly indicated (number of atoms, my stupid mistake. Cheers /Per > 24 apr. 2019 kl. 16:51 skrev Mark Abraham : > > Hi, > > Generally the REMD code has written some analysis to the log file above > this error message that should provide context. > > More generally, you can use gmx check to compare the .tpr files and observe > that the differences between them are only what you expect. > > Mark > > On Wed, 24 Apr 2019 at 15:28, Per Larsson wrote: > >> Hi gmx-users, >> >> I am trying to start a replica exchange simulation of a model peptide in >> water, but can’t get it to run properly. >> I have limited experience with REMD, so I thought I’d ask here for all the >> rookie mistakes it is possible to do. >> I have also seen the earlier discussions about the error message, but >> those seemed to be related to restarts and/or continuations, rather than >> not being able to run at all. >> >> My gromacs version is 2016 (for compatibility reasons), and the exact >> error message I get is this: >> >> --- >> Program: gmx mdrun, version 2016.5 >> Source file: src/gromacs/mdlib/main.cpp (line 115) >> MPI rank:32 (out of 62) >> >> Fatal error: >> The 62 subsystems are not compatible >> >> I followed Marks tutorial on the gromacs website and have a small >> bash-script that loops over all desired temperatures, run equilibration >> etc. >> I then start the simulation like this: >> >> $MPIRUN $GMX mdrun $ntmpi -ntomp $ntomp -deffnm sim -replex 500 -multidir >> ~pfs/ferring/gnrh_aa/dipep_remd/sim* >> >> What could be the source of this incompatibility? >> >> Many thanks >> /Per >> >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD analysis of trajectories
Hi, That's what you already have. See http://www.gromacs.org/Documentation/How-tos/REMD#Post-Processing Mark On Thu, Jun 1, 2017 at 5:37 AM YanhuaOuyang <15901283...@163.com> wrote: > Hi, >I have run a 100ns-REMD of protein, which has 20 replicas (i.e. > remd1.xtc, remd2.xtc, ..., remd20.xtc). I want to analyze a trajectory at > specific temperature such as a trajectory at experiment temperature 298K > rather than analyzing the continuous trajectory. I have known GROMACS > exchange coordinate when REMD running. Do I just analyze remd2.xtc of > replica 2(T=298K) if I want to analyze a trajectory at 298K? Do I need to > do something else on the trajectories to get a trajectory at specific > temperature(i.e. 298K)? > > Best regards, > Ouyang > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD analysis of trajectories
Do you mean that the original trajectories REMD generated are belong to "one trajectory per temperature" (i.e. the md2.xtc is a trajectory at 298K)? Ouyang At 2017-06-01 21:00:52, "Mark Abraham" wrote: >Hi, > >That's what you already have. See >http://www.gromacs.org/Documentation/How-tos/REMD#Post-Processing > >Mark > >On Thu, Jun 1, 2017 at 5:37 AM YanhuaOuyang <15901283...@163.com> wrote: > >> Hi, >>I have run a 100ns-REMD of protein, which has 20 replicas (i.e. >> remd1.xtc, remd2.xtc, ..., remd20.xtc). I want to analyze a trajectory at >> specific temperature such as a trajectory at experiment temperature 298K >> rather than analyzing the continuous trajectory. I have known GROMACS >> exchange coordinate when REMD running. Do I just analyze remd2.xtc of >> replica 2(T=298K) if I want to analyze a trajectory at 298K? Do I need to >> do something else on the trajectories to get a trajectory at specific >> temperature(i.e. 298K)? >> >> Best regards, >> Ouyang >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD analysis of trajectories
Hi, What did you learn from the first sentence of the link I gave you? Mark On Thu, Jun 1, 2017 at 3:20 PM YanhuaOuyang <15901283...@163.com> wrote: > Do you mean that the original trajectories REMD generated are belong to > "one trajectory per temperature" (i.e. the md2.xtc is a trajectory at 298K)? > > > > Ouyang > > > > > At 2017-06-01 21:00:52, "Mark Abraham" wrote: > >Hi, > > > >That's what you already have. See > >http://www.gromacs.org/Documentation/How-tos/REMD#Post-Processing > > > >Mark > > > >On Thu, Jun 1, 2017 at 5:37 AM YanhuaOuyang <15901283...@163.com> wrote: > > > >> Hi, > >>I have run a 100ns-REMD of protein, which has 20 replicas (i.e. > >> remd1.xtc, remd2.xtc, ..., remd20.xtc). I want to analyze a trajectory > at > >> specific temperature such as a trajectory at experiment temperature > 298K > >> rather than analyzing the continuous trajectory. I have known GROMACS > >> exchange coordinate when REMD running. Do I just analyze remd2.xtc of > >> replica 2(T=298K) if I want to analyze a trajectory at 298K? Do I need > to > >> do something else on the trajectories to get a trajectory at specific > >> temperature(i.e. 298K)? > >> > >> Best regards, > >> Ouyang > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > >-- > >Gromacs Users mailing list > > > >* Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > >* For (un)subscribe requests visit > >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD analysis of trajectories
Ouyang, Each Replica corresponds to 1 temperature in Gromacs (unlike other software packages). If you want to have continuous trajectories (i.e. follow the motion of one replica through temperature exchanges) then you have to demux. But the demux is really only useful (in my experience) with use of the retired g_kinetics tool. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Thursday, June 01, 2017 10:53 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] REMD analysis of trajectories Hi, What did you learn from the first sentence of the link I gave you? Mark On Thu, Jun 1, 2017 at 3:20 PM YanhuaOuyang <15901283...@163.com> wrote: > Do you mean that the original trajectories REMD generated are belong to > "one trajectory per temperature" (i.e. the md2.xtc is a trajectory at 298K)? > > > > Ouyang > > > > > At 2017-06-01 21:00:52, "Mark Abraham" wrote: > >Hi, > > > >That's what you already have. See > >http://www.gromacs.org/Documentation/How-tos/REMD#Post-Processing > > > >Mark > > > >On Thu, Jun 1, 2017 at 5:37 AM YanhuaOuyang <15901283...@163.com> wrote: > > > >> Hi, > >>I have run a 100ns-REMD of protein, which has 20 replicas (i.e. > >> remd1.xtc, remd2.xtc, ..., remd20.xtc). I want to analyze a trajectory > at > >> specific temperature such as a trajectory at experiment temperature > 298K > >> rather than analyzing the continuous trajectory. I have known GROMACS > >> exchange coordinate when REMD running. Do I just analyze remd2.xtc of > >> replica 2(T=298K) if I want to analyze a trajectory at 298K? Do I need > to > >> do something else on the trajectories to get a trajectory at specific > >> temperature(i.e. 298K)? > >> > >> Best regards, > >> Ouyang > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > >-- > >Gromacs Users mailing list > > > >* Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > >* For (un)subscribe requests visit > >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD slow's down drastically
Because every replica has to be calculated separately, it seems the speed is not that slow (125 * 0.07 ~ 9 ns). Also, to evaluate it, you should post how many CPUs you used, and other information like exchange attempt frequency... Francis On Mon, Feb 24, 2014 at 3:32 PM, Singam Karthick wrote: > Dear members, > I am trying to run REMD simulation for poly Alanine (12 residue) system. I > used remd generator to get the range of temperature with the exchange > probability of 0.3. I was getting the 125 replicas. I tried to simulate 125 > replicas its drastically slow down the simulation time (for 70 pico seconds > it took around 17 hours ) could anyone please tell me how to solve this > issue. > > Following is the MDP file > > title = G4Ga3a4a5 production. > ;define = ;-DPOSRES ; position restrain the protein > ; Run parameters > integrator = md; leap-frog integrator > nsteps = 1250 ; 2 * 500 = 3ns > dt = 0.002 ; 2 fs > ; Output control > nstxout = 0 ; save coordinates every 0.2 ps > nstvout = 1 ; save velocities every 0.2 ps > nstxtcout = 500 ; save xtc coordinate every 0.2 ps > nstenergy = 500 ; save energies every 0.2 ps > nstlog = 100 ; update log file every 0.2 ps > ; Bond parameters > continuation= yes ; Restarting after NVT > constraint_algorithm = lincs; holonomic constraints > constraints = hbonds; all bonds (even heavy atom-H bonds) > constrained > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > morse = no > ; Neighborsearching > ns_type = grid ; search neighboring grid cels > nstlist = 5 ; 10 fs > rlist = 1.0 ; short-range neighborlist cutoff (in nm) > rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) > rvdw= 1.0 ; short-range van der Waals cutoff (in nm) > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for long-range > electrostatics > pme_order = 4 ; cubic interpolation > fourierspacing = 0.16 ; grid spacing for FFT > ; Temperature coupling is on > tcoupl = V-rescale ; modified Berendsen thermostat > tc-grps = protein SOL Cl ;two coupling groups - more > accurate > tau_t = 0.1 0.1 0.1 ; time constant, in ps > ref_t = X X X; reference temperature, > one for each group, in K > ; Pressure coupling is on > pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT > pcoupltype = isotropic ; uniform scaling of box vectors > tau_p = 2.0 ; time constant, in ps > ref_p = 1.0 ; reference pressure, in bar > compressibility = 4.5e-5; isothermal compressibility of water, > bar^-1 > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > ; Dispersion correction > > DispCorr= EnerPres ; account for cut-off vdW scheme > > > regards > singam > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Zhifeng (Francis) Jing Graduate Student in Physical Chemistry School of Chemistry and Chemical Engineering Shanghai Jiao Tong University http://sun.sjtu.edu.cn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD slow's down drastically
sorry, and what performance did you expect from REMD? Dr. Vitaly V. Chaban On Mon, Feb 24, 2014 at 8:32 AM, Singam Karthick wrote: > Dear members, > I am trying to run REMD simulation for poly Alanine (12 residue) system. I > used remd generator to get the range of temperature with the exchange > probability of 0.3. I was getting the 125 replicas. I tried to simulate 125 > replicas its drastically slow down the simulation time (for 70 pico seconds > it took around 17 hours ) could anyone please tell me how to solve this issue. > > Following is the MDP file > > title = G4Ga3a4a5 production. > ;define = ;-DPOSRES ; position restrain the protein > ; Run parameters > integrator = md; leap-frog integrator > nsteps = 1250 ; 2 * 500 = 3ns > dt = 0.002 ; 2 fs > ; Output control > nstxout = 0 ; save coordinates every 0.2 ps > nstvout = 1 ; save velocities every 0.2 ps > nstxtcout = 500 ; save xtc coordinate every 0.2 ps > nstenergy = 500 ; save energies every 0.2 ps > nstlog = 100 ; update log file every 0.2 ps > ; Bond parameters > continuation= yes ; Restarting after NVT > constraint_algorithm = lincs; holonomic constraints > constraints = hbonds; all bonds (even heavy atom-H bonds) > constrained > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > morse = no > ; Neighborsearching > ns_type = grid ; search neighboring grid cels > nstlist = 5 ; 10 fs > rlist = 1.0 ; short-range neighborlist cutoff (in nm) > rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) > rvdw= 1.0 ; short-range van der Waals cutoff (in nm) > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for long-range > electrostatics > pme_order = 4 ; cubic interpolation > fourierspacing = 0.16 ; grid spacing for FFT > ; Temperature coupling is on > tcoupl = V-rescale ; modified Berendsen thermostat > tc-grps = protein SOL Cl ;two coupling groups - more accurate > tau_t = 0.1 0.1 0.1 ; time constant, in ps > ref_t = X X X; reference temperature, one > for each group, in K > ; Pressure coupling is on > pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT > pcoupltype = isotropic ; uniform scaling of box vectors > tau_p = 2.0 ; time constant, in ps > ref_p = 1.0 ; reference pressure, in bar > compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > ; Dispersion correction > > DispCorr= EnerPres ; account for cut-off vdW scheme > > > regards > singam > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD slow's down drastically
Dear Francis we are running in the Xeon E5-2670 8C 2.60GHz (2 CPUs , 8 cores, 16 threads) for each temperature. and the exchange attempt frequency is 500 steps. The other system with 126 replicas run 30 ns per day ( system size of ~38000 atoms). could you please help us in solving this problem regards singam On Monday, 24 February 2014 1:02 PM, Singam Karthick wrote: Dear members, I am trying to run REMD simulation for poly Alanine (12 residue) system. I used remd generator to get the range of temperature with the exchange probability of 0.3. I was getting the 125 replicas. I tried to simulate 125 replicas its drastically slow down the simulation time (for 70 pico seconds it took around 17 hours ) could anyone please tell me how to solve this issue. Following is the MDP file title = G4Ga3a4a5 production. ;define = ;-DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 1250 ; 2 * 500 = 3ns dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; save coordinates every 0.2 ps nstvout = 1 ; save velocities every 0.2 ps nstxtcout = 500 ; save xtc coordinate every 0.2 ps nstenergy = 500 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = yes ; Restarting after NVT constraint_algorithm = lincs ; holonomic constraints constraints = hbonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy morse = no ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = protein SOL Cl ;two coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = X X X ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme regards singam -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD slow's down drastically
Adding replicas cannot of itself slow things down, though it will increase the cost linearly. Don't try to run them all on the same amount of hardware as a smaller calculation! You are shooting yourself in the foot if you do not have at least one processor per replica (= MPI rank). Mark On Mon, Feb 24, 2014 at 8:32 AM, Singam Karthick wrote: > Dear members, > I am trying to run REMD simulation for poly Alanine (12 residue) system. I > used remd generator to get the range of temperature with the exchange > probability of 0.3. I was getting the 125 replicas. I tried to simulate 125 > replicas its drastically slow down the simulation time (for 70 pico seconds > it took around 17 hours ) could anyone please tell me how to solve this > issue. > > Following is the MDP file > > title = G4Ga3a4a5 production. > ;define = ;-DPOSRES ; position restrain the protein > ; Run parameters > integrator = md; leap-frog integrator > nsteps = 1250 ; 2 * 500 = 3ns > dt = 0.002 ; 2 fs > ; Output control > nstxout = 0 ; save coordinates every 0.2 ps > nstvout = 1 ; save velocities every 0.2 ps > nstxtcout = 500 ; save xtc coordinate every 0.2 ps > nstenergy = 500 ; save energies every 0.2 ps > nstlog = 100 ; update log file every 0.2 ps > ; Bond parameters > continuation= yes ; Restarting after NVT > constraint_algorithm = lincs; holonomic constraints > constraints = hbonds; all bonds (even heavy atom-H bonds) > constrained > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > morse = no > ; Neighborsearching > ns_type = grid ; search neighboring grid cels > nstlist = 5 ; 10 fs > rlist = 1.0 ; short-range neighborlist cutoff (in nm) > rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) > rvdw= 1.0 ; short-range van der Waals cutoff (in nm) > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for long-range > electrostatics > pme_order = 4 ; cubic interpolation > fourierspacing = 0.16 ; grid spacing for FFT > ; Temperature coupling is on > tcoupl = V-rescale ; modified Berendsen thermostat > tc-grps = protein SOL Cl ;two coupling groups - more > accurate > tau_t = 0.1 0.1 0.1 ; time constant, in ps > ref_t = X X X; reference temperature, > one for each group, in K > ; Pressure coupling is on > pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT > pcoupltype = isotropic ; uniform scaling of box vectors > tau_p = 2.0 ; time constant, in ps > ref_p = 1.0 ; reference pressure, in bar > compressibility = 4.5e-5; isothermal compressibility of water, > bar^-1 > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > ; Dispersion correction > > DispCorr= EnerPres ; account for cut-off vdW scheme > > > regards > singam > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD slow's down drastically
So what's the difference between the two systems? I think you can look through the end of the log file, and find which part slowed down. Maybe your job did not use the right partition of cores (too much comm. time)? I don't know. Francis On 25 Feb, 2014 1:19 am, "Singam Karthick" wrote: > Dear Francis > we are running in the Xeon E5-2670 8C 2.60GHz (2 CPUs , 8 cores, 16 > threads) for each temperature. and the exchange attempt frequency is 500 > steps. The other system with 126 replicas run 30 ns per day ( system size > of ~38000 atoms). could you please help us in solving this problem > > regards > singam > > > > On Monday, 24 February 2014 1:02 PM, Singam Karthick > wrote: > > Dear members, > I am trying to run REMD simulation for poly Alanine (12 residue) system. I > used remd generator to get the range of temperature with the exchange > probability of 0.3. I was getting the 125 replicas. I tried to simulate 125 > replicas its drastically slow down the simulation time (for 70 pico seconds > it took around 17 hours ) could anyone please tell me how to solve this > issue. > > Following is the MDP file > > title = G4Ga3a4a5 production. > ;define = ;-DPOSRES ; position restrain the protein > ; Run parameters > integrator = md; leap-frog integrator > nsteps = 1250 ; 2 * 500 = 3ns > dt = 0.002 ; 2 fs > ; Output control > nstxout = 0 ; save coordinates every 0.2 ps > nstvout = 1 ; save velocities every 0.2 ps > nstxtcout = 500 ; save xtc coordinate every 0.2 ps > nstenergy = 500 ; save energies every 0.2 ps > nstlog = 100 ; update log file every 0.2 ps > ; Bond parameters > continuation= yes ; Restarting after NVT > constraint_algorithm = lincs; holonomic constraints > constraints = hbonds; all bonds (even heavy atom-H bonds) > constrained > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > morse = no > ; Neighborsearching > ns_type = grid ; search neighboring grid cels > nstlist = 5 ; 10 fs > rlist = 1.0 ; short-range neighborlist cutoff (in nm) > rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) > rvdw= 1.0 ; short-range van der Waals cutoff (in nm) > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for long-range > electrostatics > pme_order = 4 ; cubic interpolation > fourierspacing = 0.16 ; grid spacing for FFT > ; Temperature coupling is on > tcoupl = V-rescale ; modified Berendsen thermostat > tc-grps = protein SOL Cl ;two coupling groups - more > accurate > tau_t = 0.1 0.1 0.1 ; time constant, in ps > ref_t = X X X; reference temperature, > one for each group, in K > ; Pressure coupling is on > pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT > pcoupltype = isotropic ; uniform scaling of box vectors > tau_p = 2.0 ; time constant, in ps > ref_p = 1.0 ; reference pressure, in bar > compressibility = 4.5e-5; isothermal compressibility of water, > bar^-1 > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > ; Dispersion correction > > DispCorr= EnerPres ; account for cut-off vdW scheme > > > regards > singam > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD slow's down drastically
Presuming that you have indeed set up the number of processors correctly (should be running on a different number of cored for different number of replicas to do a fair test), could it be a thread pinning issue? I run on a Nehalem system with 8 cores/node but, because of the Nehalem hyperthreading (I think), gromacs always complains if I run "mpirun -np $N mdrun" where $N is the number of cores NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin thread to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). However, if I use $N = 2 times the number of cores, then I don't get that note, instead getting: "Pinning threads with a logical core stride of 1" Aside, if anybody has a suggestion about how I should handle the thread pinning in my case, or if it matters, then I would be happy to hear it (my throughput seems to be good though). Finally, this comment is off topic, but you might want to reconsider having the CL ions in a separate temperature coupling group. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Singam Karthick Sent: 24 February 2014 02:32 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] REMD slow's down drastically Dear members, I am trying to run REMD simulation for poly Alanine (12 residue) system. I used remd generator to get the range of temperature with the exchange probability of 0.3. I was getting the 125 replicas. I tried to simulate 125 replicas its drastically slow down the simulation time (for 70 pico seconds it took around 17 hours ) could anyone please tell me how to solve this issue. Following is the MDP file title = G4Ga3a4a5 production. ;define = ;-DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 1250 ; 2 * 500 = 3ns dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; save coordinates every 0.2 ps nstvout = 1 ; save velocities every 0.2 ps nstxtcout = 500 ; save xtc coordinate every 0.2 ps nstenergy = 500 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= yes ; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints = hbonds; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy morse = no ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = protein SOL Cl ;two coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = X X X; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme regards singam -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD slow's down drastically
On Feb 24, 2014 11:01 PM, "Christopher Neale" wrote: > > Presuming that you have indeed set up the number of processors correctly (should be running on a different number of cored for different number of replicas to do a fair test), could it be a thread pinning issue? Yes, but part of the larger problem of over-loading the physical cores. > I run on a Nehalem system with 8 cores/node but, because of the Nehalem hyperthreading (I think), gromacs always complains if I run "mpirun -np $N mdrun" where $N is the number of cores > > NOTE: The number of threads is not equal to the number of (logical) cores > and the -pin option is set to auto: will not pin thread to cores. > This can lead to significant performance degradation. > Consider using -pin on (and -pinoffset in case you run multiple jobs). > > However, if I use $N = 2 times the number of cores, then I don't get that note, instead getting: > > "Pinning threads with a logical core stride of 1" > > Aside, if anybody has a suggestion about how I should handle the thread pinning in my case, or if it matters, then I would be happy to hear it (my throughput seems to be good though). Hyper-threading is good for applications that are memory- or user-bound (so enabled by default on consumer machines), so they can take advantage of CPU instruction-issue opportunities while stalled. GROMACS kernels are already CPU-bound, so there is little to gain and it generally does not pay for the overhead. Generally, one should not use HT; turning it off can be emulated with the right use of -pinoffset and using half the number of threads. > Finally, this comment is off topic, but you might want to reconsider having the CL ions in a separate temperature coupling group. Indeed. Mark > Chris. > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Singam Karthick > Sent: 24 February 2014 02:32 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] REMD slow's down drastically > > Dear members, > I am trying to run REMD simulation for poly Alanine (12 residue) system. I used remd generator to get the range of temperature with the exchange probability of 0.3. I was getting the 125 replicas. I tried to simulate 125 replicas its drastically slow down the simulation time (for 70 pico seconds it took around 17 hours ) could anyone please tell me how to solve this issue. > > Following is the MDP file > > title = G4Ga3a4a5 production. > ;define = ;-DPOSRES ; position restrain the protein > ; Run parameters > integrator = md; leap-frog integrator > nsteps = 1250 ; 2 * 500 = 3ns > dt = 0.002 ; 2 fs > ; Output control > nstxout = 0 ; save coordinates every 0.2 ps > nstvout = 1 ; save velocities every 0.2 ps > nstxtcout = 500 ; save xtc coordinate every 0.2 ps > nstenergy = 500 ; save energies every 0.2 ps > nstlog = 100 ; update log file every 0.2 ps > ; Bond parameters > continuation= yes ; Restarting after NVT > constraint_algorithm = lincs; holonomic constraints > constraints = hbonds; all bonds (even heavy atom-H bonds) constrained > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > morse = no > ; Neighborsearching > ns_type = grid ; search neighboring grid cels > nstlist = 5 ; 10 fs > rlist = 1.0 ; short-range neighborlist cutoff (in nm) > rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) > rvdw= 1.0 ; short-range van der Waals cutoff (in nm) > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics > pme_order = 4 ; cubic interpolation > fourierspacing = 0.16 ; grid spacing for FFT > ; Temperature coupling is on > tcoupl = V-rescale ; modified Berendsen thermostat > tc-grps = protein SOL Cl ;two coupling groups - more accurate > tau_t = 0.1 0.1 0.1 ; time constant, in ps > ref_t = X X X; reference temperature, one for each group, in K > ; Pressure coupling is on > pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT > pcoupltype = isotropic ; uniform scaling of box vectors > tau_p = 2.0 ; time constant, in ps > ref_p = 1.0 ; reference pressure, in bar > compressibility = 4.5e-5; isothermal c
Re: [gmx-users] REMD slow's down drastically
Thank you Mark for the tips about the pinoffset. I'll try it and see if it affects the speed at all. Regarding the utility of hyperthreading, running on a cluster in which each node has 8 Nehalem processing cores, I have seen 5-15% speedup from using hyperthreading via 16 threads vs. using only 8 threads (in non-MPI gromacs). This is across about 10 simulations systems that I have worked on in the last four years. In all these cases, I am using -npme 0. However, once multiple nodes and IB fabric get involved, then hyperthreading gives no benefit and generally degrades the performance. Perhaps there are some other things getting involved here, but the only change I make is mdrun -nt 8 or mdrun -nt 16 and I see a speedup from -nt 16. System sizes range from 10K to 250K atoms. Note that I have never tried using the hyperthreading with REMD or any other fancy setup. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: 24 February 2014 21:26 To: Discussion list for GROMACS users Subject: Re: [gmx-users] REMD slow's down drastically On Feb 24, 2014 11:01 PM, "Christopher Neale" wrote: > > Presuming that you have indeed set up the number of processors correctly (should be running on a different number of cored for different number of replicas to do a fair test), could it be a thread pinning issue? Yes, but part of the larger problem of over-loading the physical cores. > I run on a Nehalem system with 8 cores/node but, because of the Nehalem hyperthreading (I think), gromacs always complains if I run "mpirun -np $N mdrun" where $N is the number of cores > > NOTE: The number of threads is not equal to the number of (logical) cores > and the -pin option is set to auto: will not pin thread to cores. > This can lead to significant performance degradation. > Consider using -pin on (and -pinoffset in case you run multiple jobs). > > However, if I use $N = 2 times the number of cores, then I don't get that note, instead getting: > > "Pinning threads with a logical core stride of 1" > > Aside, if anybody has a suggestion about how I should handle the thread pinning in my case, or if it matters, then I would be happy to hear it (my throughput seems to be good though). Hyper-threading is good for applications that are memory- or user-bound (so enabled by default on consumer machines), so they can take advantage of CPU instruction-issue opportunities while stalled. GROMACS kernels are already CPU-bound, so there is little to gain and it generally does not pay for the overhead. Generally, one should not use HT; turning it off can be emulated with the right use of -pinoffset and using half the number of threads. > Finally, this comment is off topic, but you might want to reconsider having the CL ions in a separate temperature coupling group. Indeed. Mark > Chris. > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Singam Karthick > Sent: 24 February 2014 02:32 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] REMD slow's down drastically > > Dear members, > I am trying to run REMD simulation for poly Alanine (12 residue) system. I used remd generator to get the range of temperature with the exchange probability of 0.3. I was getting the 125 replicas. I tried to simulate 125 replicas its drastically slow down the simulation time (for 70 pico seconds it took around 17 hours ) could anyone please tell me how to solve this issue. > > Following is the MDP file > > title = G4Ga3a4a5 production. > ;define = ;-DPOSRES ; position restrain the protein > ; Run parameters > integrator = md; leap-frog integrator > nsteps = 1250 ; 2 * 500 = 3ns > dt = 0.002 ; 2 fs > ; Output control > nstxout = 0 ; save coordinates every 0.2 ps > nstvout = 1 ; save velocities every 0.2 ps > nstxtcout = 500 ; save xtc coordinate every 0.2 ps > nstenergy = 500 ; save energies every 0.2 ps > nstlog = 100 ; update log file every 0.2 ps > ; Bond parameters > continuation= yes ; Restarting after NVT > constraint_algorithm = lincs; holonomic constraints > constraints = hbonds; all bonds (even heavy atom-H bonds) constrained > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > morse = no > ; Neighborsearching > ns_type = grid ; search neighboring grid cels > nstlist = 5 ; 10 fs > rlist
Re: [gmx-users] REMD slow's down drastically
Goods to know, thanks. Mileage certainly does vary. Mark On Feb 25, 2014 3:45 AM, "Christopher Neale" wrote: > Thank you Mark for the tips about the pinoffset. I'll try it and see if it > affects the speed at all. > > Regarding the utility of hyperthreading, running on a cluster in which > each node has 8 Nehalem processing cores, I have seen 5-15% speedup from > using hyperthreading via 16 threads vs. using only 8 threads (in non-MPI > gromacs). This is across about 10 simulations systems that I have worked on > in the last four years. In all these cases, I am using -npme 0. However, > once multiple nodes and IB fabric get involved, then hyperthreading gives > no benefit and generally degrades the performance. Perhaps there are some > other things getting involved here, but the only change I make is mdrun -nt > 8 or mdrun -nt 16 and I see a speedup from -nt 16. System sizes range from > 10K to 250K atoms. Note that I have never tried using the hyperthreading > with REMD or any other fancy setup. > > Chris. > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark > Abraham > Sent: 24 February 2014 21:26 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] REMD slow's down drastically > > On Feb 24, 2014 11:01 PM, "Christopher Neale" < > chris.ne...@alum.utoronto.ca> > wrote: > > > > Presuming that you have indeed set up the number of processors correctly > (should be running on a different number of cored for different number of > replicas to do a fair test), could it be a thread pinning issue? > > Yes, but part of the larger problem of over-loading the physical cores. > > > I run on a Nehalem system with 8 cores/node but, because of the Nehalem > hyperthreading (I think), gromacs always complains if I run "mpirun -np $N > mdrun" where $N is the number of cores > > > > NOTE: The number of threads is not equal to the number of (logical) cores > > and the -pin option is set to auto: will not pin thread to cores. > > This can lead to significant performance degradation. > > Consider using -pin on (and -pinoffset in case you run multiple > jobs). > > > > However, if I use $N = 2 times the number of cores, then I don't get that > note, instead getting: > > > > "Pinning threads with a logical core stride of 1" > > > > Aside, if anybody has a suggestion about how I should handle the thread > pinning in my case, or if it matters, then I would be happy to hear it (my > throughput seems to be good though). > > Hyper-threading is good for applications that are memory- or user-bound (so > enabled by default on consumer machines), so they can take advantage of CPU > instruction-issue opportunities while stalled. GROMACS kernels are already > CPU-bound, so there is little to gain and it generally does not pay for the > overhead. Generally, one should not use HT; turning it off can be emulated > with the right use of -pinoffset and using half the number of threads. > > > Finally, this comment is off topic, but you might want to reconsider > having the CL ions in a separate temperature coupling group. > > Indeed. > > Mark > > > Chris. > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Singam > Karthick > > Sent: 24 February 2014 02:32 > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: [gmx-users] REMD slow's down drastically > > > > Dear members, > > I am trying to run REMD simulation for poly Alanine (12 residue) system. > I used remd generator to get the range of temperature with the exchange > probability of 0.3. I was getting the 125 replicas. I tried to simulate 125 > replicas its drastically slow down the simulation time (for 70 pico seconds > it took around 17 hours ) could anyone please tell me how to solve this > issue. > > > > Following is the MDP file > > > > title = G4Ga3a4a5 production. > > ;define = ;-DPOSRES ; position restrain the protein > > ; Run parameters > > integrator = md; leap-frog integrator > > nsteps = 1250 ; 2 * 500 = 3ns > > dt = 0.002 ; 2 fs > > ; Output control > > nstxout = 0 ; save coordinates every 0.2 ps > > nstvout = 1 ; save velocities every 0.2 ps > > nstxtcout = 500 ; save xtc coordinate every
[gmx-users] REMD on more than one node
Hi, I am running a REMD with grimacs 5.0, I have 46 replica, 4 nodes, 16 cores per node. how can I use my compute resource and what’s the command of “gmx mdrun”? the command is below, I am not sure weather it is right mpirun -np 4 -npme gmx mdrun -s md_01.tpr -multi 46 -replex 500 -reseed -1. mpirun -np 4 -npme gmx mdrun -s md_02.tpr -multi 46 -replex 500 -reseed -1. mpirun -np 4 -npme gmx mdrun -s md_03.tpr -multi 46 -replex 500 -reseed -1. … mpirun -np 4 -npme gmx mdrun -s md_46.tpr -multi 46 -replex 500 -reseed -1. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
