Re: [gmx-users] profiles az a function of z
Paymon Pirzadeh wrote: Well, the main purpose is to average the energy or any desired property along any desired coordinate axis. simple binning of the box will do the job, but I was wondering if this can be done in general with gromacs post simulation tools. No, there is no general way to do this. Individual tools might let you construct various analysis "groups" according to some geometric criterion, but in general you need to use atomic indices in .ndx files. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] reduced units
Dear, I want to do stochastic simulations in the framework of Langevin dynamics using Gromacs with the reduced units. The questions are: 1. How to turn on the reduced units? Is there any parameters for setting? 2. If I use the reduced temperature of 1, should the ref_t in the .mdp file be the 120.2717 ? Right? 3. I create the force field(.itp and .top) within the reduced units myself. Are there any suggestion for avoiding errors? Thanks in advance. -- wende ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Example file for DNA
David Crosby wrote: Hello fellow GROMACS users! I've been having a heck of a time with the reformatting of a DNA molecule into a GROMACS-compatible format. I know that residues (bases) must be renamed to DTHR, etc., though it would be endlessly helpful if someone could please send me an example pdb or gmx file I can use as reference. Better yet, if anyone has a nifty program that will reformat a nucleic acid model into the GROMACS format, that would answer my prayers! The duplex I'm working with is only 21nt, so it's not insane to have to modify the file by hand... A simple Perl script can make substitutions, or you can use a text editor like vi or a command like sed. In about 4 commands, the whole file can be re-named. In vi, for example: :1,$s/DT /DTHY/g ...and all of your thymines are re-named (note the spacing is important). -Justin Thanks in advance! Dave Crosby University of California, Irvine Dept of Pathology and Laboratory Medicine ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Example file for DNA
Hello fellow GROMACS users! I've been having a heck of a time with the reformatting of a DNA molecule into a GROMACS-compatible format. I know that residues (bases) must be renamed to DTHR, etc., though it would be endlessly helpful if someone could please send me an example pdb or gmx file I can use as reference. Better yet, if anyone has a nifty program that will reformat a nucleic acid model into the GROMACS format, that would answer my prayers! The duplex I'm working with is only 21nt, so it's not insane to have to modify the file by hand... Thanks in advance! Dave Crosby University of California, Irvine Dept of Pathology and Laboratory Medicine ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] profiles az a function of z
Well, the main purpose is to average the energy or any desired property along any desired coordinate axis. simple binning of the box will do the job, but I was wondering if this can be done in general with gromacs post simulation tools. Payman On Fri, 2009-10-16 at 16:05 -0400, Justin A. Lemkul wrote: > > Paymon Pirzadeh wrote: > > Hello, > > In a simulation, how is it possible to extract the profiles e.g. > > potential as a function of z (coordinate axis of box)? > > > > g_potential can do this for electrostatic potential, but I don't know about > anything else. I don't think it is a trivial question to decompose the > potential of the entire system along any axis. > > -Justin > > > Payman > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > > ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] profiles az a function of z
Paymon Pirzadeh wrote: Hello, In a simulation, how is it possible to extract the profiles e.g. potential as a function of z (coordinate axis of box)? g_potential can do this for electrostatic potential, but I don't know about anything else. I don't think it is a trivial question to decompose the potential of the entire system along any axis. -Justin Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] GROMACS scaling at 64 cpus
Hi, This of course depends very much on all your settings. Up to now I have found that a 3:1 ratio is optimal for rectangular boxes, whereas 2:1 is optimal for rhombic dodecahedra. 64 cores was the limit for the benchmark system on that hardware, so I had to increase the number of PME beyond the 1/3 to get optimal performance. Berk Hi, I recently got a nice Sun X6275 blade system http://nf.nci.org.au/facilities/vayu/hardware.php (ok, not just for me!) whose hardware ought to be better, but very comparable to that used in the GROMACS 4 paper (http://pubs.acs.org/doi/abs/10.1021/ct700301q). Figure 5 there demonstrates good scaling out to 38 cpus, but it drops away from linearity by 64. On the same test system on this hardware (pdf attached; blue arrow is ideal linearity) the drop-off is still about the same. For 64 cpus, that paper reports using 28 PME nodes, which is an appreciably lower ratio than the 2:1 for the rest of the tests. On my hardware I found that that choice cost about 30% performance, compared with a more reasonable use of 19 PME nodes (64 vs 86 ns/day, pdf attached). Is that 28 a typo for 18? Mark _ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] profiles az a function of z
Hello, In a simulation, how is it possible to extract the profiles e.g. potential as a function of z (coordinate axis of box)? Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Lipid-protein tutorial by Lemkul
Hi Justin, Thank you for your answer. It made me to think again and I found the source of the problem (silly mistake). Thanks again! Seunghwan Lee --- On Fri, 10/16/09, Justin A. Lemkul wrote: > From: Justin A. Lemkul > Subject: Re: [gmx-users] Lipid-protein tuturial by Lemkul > To: "Discussion list for GROMACS users" > Date: Friday, October 16, 2009, 11:45 AM > > > seunghwan lee wrote: > > Hi > > > > I am new to Gromacs and going through some tutorials. > I am working on lipid-protein tutorial given by Justin > Lemkul and I am stuck with the very first step. When I > execute pdb2gmx to generate .top file and .pdb without > hydrogen, > > > > pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro > -ignh -ter -water spc > > > > I got the following message: > > > > > --- > > Program pdb2gmx, VERSION 4.0.4 > > Source code file: pgutil.c, line: 87 > > > > Fatal error: > > Atom H not found in residue 17 while adding improper > > > > > --- > > > > I made the correction to ffG53a6.rtp file as suggested > by Justin, but apparently I am still having a problem with > -NH2 residue (#17). Is there any other corrections I need to > do in order to make this work? > > > > No other correction is necessary. If you fixed the > .rtp file correctly, you should not have any problems. > > -Justin > > > Thanks for your help!! > > Seunghwan Lee > > > > > > >___ > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > > > -- > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Error during NVT equillibration with nvt.log file
ram bio wrote: Dear Justin, Thanks and I tried your suggestion, that is minimizing the system without restraints and increasing the Fmax to 1000, the mdp file used is as follows: Note that I only suggested EM, not necessarily Fmax < 1000. You original post contained an even lower Fmax, suggesting that you can do better than 1000. The parameters in my tutorial are somewhat generic; you should alter them to suit your needs. Please note that the headers of log files are typically unnecessary when posting the .mdp file. please suggest me is it ok to remove the constraints and run the NVT equillibration. You can try it, but I doubt it will make a difference. Your simulation is crashing before it is even starting, making it very difficult to diagnose. You probably need to re-build the system, using as rigorous criteria as possible during the InflateGRO steps to ensure that you don't have any improper atomic overlap. In my experience, if the simulation is failing at step 0, there is no hope for coaxing the system into working. The configuration simply isn't reasonable. -Justin Thanks Ram On Fri, Oct 16, 2009 at 9:27 PM, Justin A. Lemkul wrote: ram bio wrote: Dear Gromacs users, I am doing protein in lipid-bilayer simulation and i am following the procedure as per justin tutorial. I am able to insert the protein in lipid bilayer and minimize the system as per Inflategro procedure,during the total procedure the system was minimized in every step.Then, I solvated and ionized sytem and minimized using the following mdp file: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save define = -DSTRONG_POSRES integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 500.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.2 ; Short-range electrostatic cut-off rvdw= 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) the output was as follows: Steepest Descents converged to Fmax < 500 in 4770 steps Potential Energy = -3.8820288e+05 Maximum force = 4.4803549e+02 on atom 3573 Norm of force = 1.7854408e+01 As the potential energy and Fmax values were agreeable , I proceeded to equillibrate the system using NVT. Did you minimize the structure without restraints, prior to NVT? Angle G96AngleProper Dih. Ryckaert-Bell. Improper Dih. 2.20077e+048.54042e+036.78950e+034.34650e+033.03266e+03 LJ-14 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) 4.76527e+035.50236e+048.36617e+06 -2.20019e+03 -4.46844e+05 Coul. recip. Position Rest. PotentialKinetic En. Total Energy -1.65524e+051.07769e+017.85612e+065.88813e+105.88892e+10 Conserved En.Temperature Pressure (bar) Cons. rmsd () 5.88892e+102.23805e+081.21713e+093.10245e+01 In my experience, the combination of an astronomically high temperature and a repulsive temperature is indicative of restraining an unrestrainable starting structure. Try the EM I suggested above. Other than that, as I've suggested before, see the Advanced Troubleshooting page I created in the tutorial. -Justin Please help me to proceed further and let me know where are the mistakes lying and how to overcome them. Thanks in advance, Ram ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt
Re: [gmx-users] Error during NVT equillibration with nvt.log file
Dear Justin, Thanks and I tried your suggestion, that is minimizing the system without restraints and increasing the Fmax to 1000, the mdp file used is as follows: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.2 ; Short-range electrostatic cut-off rvdw= 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) and the ouput is : Steepest Descents converged to Fmax < 1000 in 1192 steps Potential Energy = -4.5402134e+05 Maximum force = 9.6024463e+02 on atom 3573 Norm of force = 3.8811920e+01 Later is used this as input for the NVT equillibration with the following nvt.mdp file: title = NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; 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 DPPC SOL_CL- ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 323 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_CL- and the ouput nvt.log file is as under: Input Parameters: integrator = md nsteps = 5 init_step= 0 ns_type = Grid nstlist = 5 ndelta = 2 nstcomm = 1 comm_mode= Linear nstlog = 100 nstxout = 100 nstvout = 100 nstfout = 0 nstenergy= 100 nstxtcout= 0 init_t = 0 delta_t = 0.002 xtcprec = 1000 nkx = 48 nky = 48 nkz = 60 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = FALSE ePBC = xyz bPeriodicMols= FALSE bContinuation= FALSE bShakeSOR= FALSE etc = V-rescale epc = No epctype = Isotropic tau_p
Re: [gmx-users] Error during NVT equillibration with nvt.log file
ram bio wrote: Dear Gromacs users, I am doing protein in lipid-bilayer simulation and i am following the procedure as per justin tutorial. I am able to insert the protein in lipid bilayer and minimize the system as per Inflategro procedure,during the total procedure the system was minimized in every step.Then, I solvated and ionized sytem and minimized using the following mdp file: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save define = -DSTRONG_POSRES integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 500.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.2 ; Short-range electrostatic cut-off rvdw= 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) the output was as follows: Steepest Descents converged to Fmax < 500 in 4770 steps Potential Energy = -3.8820288e+05 Maximum force = 4.4803549e+02 on atom 3573 Norm of force = 1.7854408e+01 As the potential energy and Fmax values were agreeable , I proceeded to equillibrate the system using NVT. Did you minimize the structure without restraints, prior to NVT? Angle G96AngleProper Dih. Ryckaert-Bell. Improper Dih. 2.20077e+048.54042e+036.78950e+034.34650e+033.03266e+03 LJ-14 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) 4.76527e+035.50236e+048.36617e+06 -2.20019e+03 -4.46844e+05 Coul. recip. Position Rest. PotentialKinetic En. Total Energy -1.65524e+051.07769e+017.85612e+065.88813e+105.88892e+10 Conserved En.Temperature Pressure (bar) Cons. rmsd () 5.88892e+102.23805e+081.21713e+093.10245e+01 In my experience, the combination of an astronomically high temperature and a repulsive temperature is indicative of restraining an unrestrainable starting structure. Try the EM I suggested above. Other than that, as I've suggested before, see the Advanced Troubleshooting page I created in the tutorial. -Justin Please help me to proceed further and let me know where are the mistakes lying and how to overcome them. Thanks in advance, Ram ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Lipid-protein tuturial by Lemkul
seunghwan lee wrote: Hi I am new to Gromacs and going through some tutorials. I am working on lipid-protein tutorial given by Justin Lemkul and I am stuck with the very first step. When I execute pdb2gmx to generate .top file and .pdb without hydrogen, pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc I got the following message: --- Program pdb2gmx, VERSION 4.0.4 Source code file: pgutil.c, line: 87 Fatal error: Atom H not found in residue 17 while adding improper --- I made the correction to ffG53a6.rtp file as suggested by Justin, but apparently I am still having a problem with -NH2 residue (#17). Is there any other corrections I need to do in order to make this work? No other correction is necessary. If you fixed the .rtp file correctly, you should not have any problems. -Justin Thanks for your help!! Seunghwan Lee ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Error during NVT equillibration with nvt.log file
Dear Gromacs users, I am doing protein in lipid-bilayer simulation and i am following the procedure as per justin tutorial. I am able to insert the protein in lipid bilayer and minimize the system as per Inflategro procedure,during the total procedure the system was minimized in every step.Then, I solvated and ionized sytem and minimized using the following mdp file: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save define = -DSTRONG_POSRES integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 500.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.2 ; Short-range electrostatic cut-off rvdw= 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) the output was as follows: Steepest Descents converged to Fmax < 500 in 4770 steps Potential Energy = -3.8820288e+05 Maximum force = 4.4803549e+02 on atom 3573 Norm of force = 1.7854408e+01 As the potential energy and Fmax values were agreeable , I proceeded to equillibrate the system using NVT. The mdp file used for NVT equillibration is : title = NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; 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 DPPC SOL_CL- ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 323 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_CL- and the output error for the mdrun is as under: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002307, max 0.080808 (between atoms 3569 and 3570) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'Protein in DPPC in water' 5 steps,100.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 31.024508, max 1431.875854 (between atoms 448 and 450) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 453455 49.90.1331 0.2004 0.1330 453454 50.50.1231 0.1762 0.1230 451452 89.90.1003 29.4775 0
[gmx-users] Error during NVT equillibration
Dear Gromacs users, I am doing protein in lipid-bilayer simulation and i am following the procedure as per justin tutorial. I am able to insert the protein in lipid bilayer and minimize the system as per Inflategro procedure,during the total procedure the system was minimized in every step.Then, I solvated and ionized sytem and minimized using the following mdp file: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save define = -DSTRONG_POSRES integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 500.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.2 ; Short-range electrostatic cut-off rvdw= 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) the output was as follows: Steepest Descents converged to Fmax < 500 in 4770 steps Potential Energy = -3.8820288e+05 Maximum force = 4.4803549e+02 on atom 3573 Norm of force = 1.7854408e+01 As the potential energy and Fmax values were agreeable , I proceeded to equillibrate the system using NVT. The mdp file used for NVT equillibration is : title = NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; 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 DPPC SOL_CL- ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 323 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_CL- and the output error for the mdrun is as under: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002307, max 0.080808 (between atoms 3569 and 3570) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'Protein in DPPC in water' 5 steps,100.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 31.024508, max 1431.875854 (between atoms 448 and 450) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 453455 49.90.1331 0.2004 0.1330 453454 50.50.1231 0.1762 0.1230 451452 89.90.1003 2
[gmx-users] Lipid-protein tuturial by Lemkul
Hi I am new to Gromacs and going through some tutorials. I am working on lipid-protein tutorial given by Justin Lemkul and I am stuck with the very first step. When I execute pdb2gmx to generate .top file and .pdb without hydrogen, pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc I got the following message: --- Program pdb2gmx, VERSION 4.0.4 Source code file: pgutil.c, line: 87 Fatal error: Atom H not found in residue 17 while adding improper --- I made the correction to ffG53a6.rtp file as suggested by Justin, but apparently I am still having a problem with -NH2 residue (#17). Is there any other corrections I need to do in order to make this work? Thanks for your help!! Seunghwan Lee ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Water molecule starting at atom X can not be settled; can't find a solution
Hi Simone, The temperature coupling might be a cause for an error like that to occur. Try to understand that coupling ions separately may cause large fluctuations in there velocities and hence cause sudden large displacements that may put an ion on top of a solvent molecule that can't be settled anymore due to that. I assume you fixed that error, but think it's good to have a bit of background (and please read some more) to help avoiding such mistakes later on. If the problem persists while the T-coupling error is fixed, then there's something else wrong :) Is it always the same water molecule, or are they always in the neighbourhood, or does the error occur at random water molecules? Is the water molecule close to the edge of the box when the error occurs? Since you have all frames, you can easily check the trajectory all the way :) You may also try running with NVT to see whether that fixes the problem. Did you actually equilibrate the temperature first, before putting the pressure on? O, and you might want to show your md.mdp, as that's where the simulation is breaking. Hope it helps, Tsjerk On Fri, Oct 16, 2009 at 1:49 PM, Justin A. Lemkul wrote: > > > Simone Cirri wrote: >> >> Justin A. Lemkul wrote: >> >> ; Berendsen temperature coupling is on in three groups >> Tcoupl = berendsen >> >> tau_t = 0.1 0.1 0.1 tc-grps = protein sol NA+ >> >> ref_t = 300 300 300 >> >> Never couple solvent and ions separately. Surely grompp warned you >> that you should be using "Protein Non-Protein"? See here: >> >> http://www.gromacs.org/Documentation/Terminology/Thermostats >> >> >> Hi Justin, thanks for the suggestion. Actually, it's an error I've always >> been doing and I'm glad I've solved it. >> However, I'm afraid it has nothing to do with the problem, because I just >> tried to run the MD again (after modifying the md.mdp as you told me) and >> the fatal error is still there. >> I've noticed the the T-coupling mistake is also in pr.mdp. Do you think >> that correcting it and re-running the PR simulation would fix the "water >> molecule can not be settled" problem? > > It's probably worth a shot. It's not appropriate to couple solvent and ions > separately in any phase, equilibration or data collection. > > -Justin > >> Anyway here is the pr.mdp (as it was before): >> >> title = hsacyx >> warnings = 10 >> cpp = /lib/cpp >> define = -DPOSRES >> constraints = all-bonds >> integrator = md >> dt = 0.002 ; ps ! >> nsteps = 10 ; total 200.0 ps. >> nstcomm = 1 >> nstxout = 250 >> nstvout = 1000 >> nstfout = 0 >> nstlog = 10 >> nstenergy = 10 >> nstlist = 10 >> ns_type = grid >> rlist = 0.9 >> coulombtype = PME >> rcoulomb = 0.9 >> rvdw = 0.9 >> fourierspacing = 0.12 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order = 6 >> ewald_rtol = 1e-5 >> optimize_fft = yes >> ; Berendsen temperature coupling is on in four groups >> Tcoupl = berendsen >> tau_t = 0.1 0.1 0.1 >> tc-grps = Protein SOL NA+ >> ref_t = 300 300 300 >> ; Pressure coupling is on >> Pcoupl = berendsen >> pcoupltype = isotropic >> tau_p = 0.5 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> ; Generate velocites is on at 300 K. >> gen_vel = yes >> gen_temp = 300.0 >> gen_seed = 173529 >> >> Thank you >> >> Simone Cirri >> >> >> >> >> ___ >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > ___ > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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'
Re: [gmx-users] Water molecule starting at atom X can not be settled; can't find a solution
Simone Cirri wrote: Justin A. Lemkul wrote: ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps = protein sol NA+ ref_t = 300 300 300 Never couple solvent and ions separately. Surely grompp warned you that you should be using "Protein Non-Protein"? See here: http://www.gromacs.org/Documentation/Terminology/Thermostats Hi Justin, thanks for the suggestion. Actually, it's an error I've always been doing and I'm glad I've solved it. However, I'm afraid it has nothing to do with the problem, because I just tried to run the MD again (after modifying the md.mdp as you told me) and the fatal error is still there. I've noticed the the T-coupling mistake is also in pr.mdp. Do you think that correcting it and re-running the PR simulation would fix the "water molecule can not be settled" problem? It's probably worth a shot. It's not appropriate to couple solvent and ions separately in any phase, equilibration or data collection. -Justin Anyway here is the pr.mdp (as it was before): title = hsacyx warnings= 10 cpp = /lib/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 10; total 200.0 ps. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype= PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing= 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order= 6 ewald_rtol= 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.10.1 tc-grps= Protein SOLNA+ ref_t = 300 300300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Thank you Simone Cirri ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] question about all atoms lipid molecule
Hi, I need to do an all atom simulation for dppc bilayer . You are right the dppc molecule file that i have has PALM and PCGL residues. Well, I don't know where you got the dppc molecule from, I thought you said you didn't have any DPPC structure with hydrogens? Anyway, I'll send you the current version of the charmm force field for GROMACS (in a separate e-mail) but I'm afraid I cannot help you in building the residue. I think it might be quite a lot of work if you don't know how CHARMM is doing it. My suggestion is that you search/ask the CHARMM mailing list for how DPPC is constructed. I will like to try to set up the charmm FF for gromacs. But I dont have the FF files with me, neither do i have the programs. Could you send me a tutorial or some reference link too ( if you know of any). What you need for running CHARMM ff in GROMACS are the files I'll send you and the latest version of the source code (i.e. do a git pull and recompile). /Pär___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Water molecule starting at atom X can not be settled; can't find a solution
Justin A. Lemkul wrote: ; Berendsen temperature coupling is on in three groups > Tcoupl = berendsen > > tau_t = 0.1 0.1 0.1 tc-grps = protein sol NA+ > > ref_t = 300 300 300 > > Never couple solvent and ions separately. Surely grompp warned you that you > should be using "Protein Non-Protein"? See here: > > http://www.gromacs.org/Documentation/Terminology/Thermostats > > Hi Justin, thanks for the suggestion. Actually, it's an error I've always been doing and I'm glad I've solved it. However, I'm afraid it has nothing to do with the problem, because I just tried to run the MD again (after modifying the md.mdp as you told me) and the fatal error is still there. I've noticed the the T-coupling mistake is also in pr.mdp. Do you think that correcting it and re-running the PR simulation would fix the "water molecule can not be settled" problem? Anyway here is the pr.mdp (as it was before): title = hsacyx warnings= 10 cpp = /lib/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 10; total 200.0 ps. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype= PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing= 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order= 6 ewald_rtol= 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.10.1 tc-grps= Protein SOLNA+ ref_t = 300 300300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Thank you Simone Cirri ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Water molecule starting at atom X can not be settled; can't find a solution
Simone Cirri wrote: ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps= protein sol NA+ ref_t = 300 300 300 Never couple solvent and ions separately. Surely grompp warned you that you should be using "Protein Non-Protein"? See here: http://www.gromacs.org/Documentation/Terminology/Thermostats -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Water molecule starting at atom X can not be settled; can't find a solution
Hi everyone, in the last weeks I've been trying to run a simulation with Gromacs 4.0.5 and the force field ffamber99. The protein is albumine (BSA, bovine serum albumine), so it's a very big one (570+ residues). The solvent is tip3p. After an energy minimization run and a position restraint run, I start with the "real" simulation. Invariably, it crashes after 1 ps with the error message: t = 1.000 ps: Water molecule starting at atom 42031 can not be settled. Check for bad contacts and/or reduce the timestep. I've searched in the mailing list and I've tried many of the solutions you proposed: - I looked at the water molecule with the problematic atom to see if it was interacting in some weird way with the protein (I put ntsxout = 1 in order to have many more frames); but it isn't so, since that molecule is only one of the many solvent molecules that (at least in the first ps) stay far from the protein - I tried to run a longer and stronger minimization: so I increased the number of steps (from 1 to 2) and I decreased emtol (from 100 to 1), but nothing changed - I tried to increase the box dimensions; in editconf I put -c 1.2 (instead of 0.7), but nothing changed. - I checked the stepXXXb.pdb and stepXXXc.pdb that mdrun created after the crash, but I didn't see anything strange in them. - I did a longer position restraint run (3 ns instead of the usual 200 ps) but nothing changed... I was hoping that it would stabilize the water, but I think the problem is not that. Even though the energy minimization doesn't show any problems, I think that's the crucial part; as someone said in another message, the problem doesn't really involve the water molecule that cannot be settled, but other atoms in the protein with big forces that in some way collide with the water molecule... am I right? In this case, deleting the problematic water molecule could help? I thought it would be useless, since that molecule is not close to the protein at all... Here you have the em.mdp and the md.mdp, if you want I can also paste the pr.mdp . title = hsacyx cpp = /lib/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002; ps ! nsteps = 2 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype= PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing= 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order= 6 ewald_rtol= 1e-5 optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 1 emstep = 0.01 title = hsacyx cpp = /lib/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 750; total 15000 ps. nstcomm = 1 nstxout = 2500 nstvout = 0 nstfout = 0 nstlist = 500 ns_type = grid rlist = 0.9 coulombtype= PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing= 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order= 6 ewald_rtol= 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps= protein sol NA+ ref_t = 300 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 I really don't know what else I could do... if someone has an idea, I would be glad to hear it. Thank you Simone Cirri PhD student at the Structural Biology Lab of University of Siena, Italy ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Coarse-Grain: GROMACS bond information to VMD
Dear all, is there any possibility to give the bond information out of GROMACS files to VMD? Especially for coarse-grained models (using the MARTINI FF) this would be a nice feature for visualization. But in that case the distance analysis doesn't work, because we will always have too high distances between two particles (CG scale). If I use "Dynamic Bonds" (as described in this thread: http://oldwww.gromacs.org/pipermail/gmx-users/2008-September/036124.html) VMD draws bonds also between non-bonded particles. I know that there is no official solutions for this (http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD), but maybe anybody of you has a script to convert *.top/*.itp/*.rtp files with a corresponding *.gro file into the PDB format with connectivity section or into the (NAMD) *.psf format. (?) The solution that I've found (top2psd.pl) is not smart enough because it's a simple 1-to-1 conversion of GROMACS topology files and has not the ability to replicate (and renumber) the topological data of single molecules (http://baaden.free.fr/soft/compchem.html). Thanks for your help... Thomas -- Thomas H. Schmidt, PhD student Computational Structural Biology Chair of Life Science Informatics, B-IT LIMES-Institute, University of Bonn Dahlmannstrasse 2, D-53113 Bonn, Germany Phone: +49-(0)228-2699 323 Fax: +49-(0)228-2699 341 http://www.csb.bit.uni-bonn.de ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] LAM OpenMPI conflict?
For your information, the procedure is: $ grompp ... (to generate minimize.tpr) $ lamboot $ l$ mdrun_mpi -np 4 -v -s minimize.tpr -o mod21_traj.trr -c mod21.gro -e mod21_ener.edr It worked nicely, exactly as the serial run "mdrun -v -s minimize.tpr ...". No interference with installed openmpi, no need to mention lam in the md command line. Forget about the Debian compilation, it does not require any special command. Have a nice day francesco On Thu, Oct 15, 2009 at 7:55 PM, Jussi Lehtola wrote: > On Thu, 2009-10-15 at 18:23 +0200, Francesco Pietra wrote: >> Hi: I was trying to minimize in vacuum a pure CG protein on a four >> core (two dual operons), getting errors: >> >> $ lamboot >> >> $ mpirun -np 4 mdrun -s mod21.tpr -o minim_mod21_traj.trr -c >> minim_mod21.gro -e minim_mod21_ener.edr >> ... >> ... >> >> WARNING: Writing ompirun noticed that job rank 2 with PID 4385 on node >> tya64 exited on signal 11 (Segmentation fault). >> 3 processes killed (possibly by Open MPI) >> Writing out atom name (SCSP1) longer than 4 characters to .pdb file > > This looks like you are trying to run the LAM binary with Open MPI's > mpirun command. Use the LAM version instead (mpirun.lam in Debian). > > Furthermore, the Debian packages use suffixes, for instance the binaries > in the gromacs-lam package are /usr/bin/mdrun_mpi.lam > and /usr/bin/mdrun_mpi_d.lam, so you should switch mdrun to > mdrun_mpi.lam . So all in all: > > $ mpirun.lam -np 4 mdrun_mpi.lam -s mod21.tpr -o minim_mod21_traj.trr -c > minim_mod21.gro -e minim_mod21_ener.edr > > What is also possible is that your installation of the Intel compiled > Open MPI is visible in your environment, which may quite well lead into > problems. > > (Also, LAM has been obsoleted by Open MPI years ago, so you might just > try switching from LAM to Open MPI, then you wouldn't have to run > lamboot at the beginning.) > -- > -- > Jussi Lehtola, FM, Tohtorikoulutettava > Fysiikan laitos, Helsingin Yliopisto > jussi.leht...@helsinki.fi, p. 191 50632 > -- > Mr. Jussi Lehtola, M. Sc., Doctoral Student > Department of Physics, University of Helsinki, Finland > jussi.leht...@helsinki.fi > -- > > > ___ > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] a bit strange errors
Dear Berk, In fact, I calculated the potential and force from the analytical function of angles in degrees, which is multicentred Gaussian-based potentials. So I think it must be some other reasons that cause the issues. Anyway, thanks again for your reply. Best wishes, Chaofu Wu, Dr. From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] a bit strange errors Date: Fri, 16 Oct 2009 09:39:07 +0200 Hi, But there could be a very similar issue there for the conversion from radians to degrees. The force has to be in units of kJ/mol/degree, not kJ/mol/radian. Berk From: xiaowu...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] a bit strange errors Date: Fri, 16 Oct 2009 15:35:19 +0800 Dear Berk, Unfortunately, this time it is angle (table_a0.xvg) that cause the problem. The angles are taken in degrees. I think it is not due to the wrong unit. Anyway, thanks very much for your reply. Best wishes, Chaofu Wu, Dr. From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] a bit strange errors Date: Fri, 16 Oct 2009 09:21:18 +0200 Hi, Last week another user reported very similar problems (also 164% deviations, I think). In that case it seemed that the user did an Angstrom to nm conversion in the table file on x without scaling f(x). Could this also be your issue? Berk From: xiaowu...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] a bit strange errors Date: Fri, 16 Oct 2009 14:55:40 +0800 Dear Mark, Thank you very much for the quick reply to my post. According to your suggestion, I check the table and reformat it with equal spacing between entries. I also check the entries calculated from the analytical functions and no wrong values are found. However, the same warnings are given, which lead to terminate the simulation. Are there any other reasons responsible for it? Best wishes, Chaofu Wu, Dr. > Date: Fri, 16 Oct 2009 14:18:17 +1100 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] a bit strange errors > > wuxiao wrote: > > Dear GMXers, > > Recently, I has been performing coarse-grained MD simulations based > > on the tabulated potentials using GROMACS. In the initialization, some > > warnings are given as follows > > /WARNING: For the 999 non-zero entries for table 0 in table_b0.xvg the > > forces deviate on average 164% from minus the numerical derivative of > > the potential/ > > This looks like your table has either wrong values or wrong formatting. > It does have to have equal spacing between entries. > > > It proceeds untill at about 17 ns before it is interupted with some errors > > /WARNING: 1-4 interaction between 148 and 151 at distance 13.125 which > > > > is larger than the 1-4 table size 2.000 nm/ > > I think the duartion time is long enough to equilibrated the system, > > which is confirmed by the energy plot with time. Why it happens so? What > > should I do to cope with this problem? Thanks a lot for any reply to > > Perhaps much of the table is fine, and the problem only arises when you > get a force being looked up in an erroneous part. > > Mark > ___ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php 使用新一代 Windows L iv e Messenger 轻松交流和共享！ 立刻下载！ What can you do with the new Windows Live? Find out 更多热辣资讯尽在新版MSN首页！ 立刻访问！ Express yourself instantly with MSN Messenger! MSN Messenger _ MSN十周年庆典，查看MSN注册时间，赢取神秘大奖 http://10.msn.com.cn___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] a bit strange errors
Hi, But there could be a very similar issue there for the conversion from radians to degrees. The force has to be in units of kJ/mol/degree, not kJ/mol/radian. Berk From: xiaowu...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] a bit strange errors Date: Fri, 16 Oct 2009 15:35:19 +0800 Dear Berk, Unfortunately, this time it is angle (table_a0.xvg) that cause the problem. The angles are taken in degrees. I think it is not due to the wrong unit. Anyway, thanks very much for your reply. Best wishes, Chaofu Wu, Dr. From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] a bit strange errors Date: Fri, 16 Oct 2009 09:21:18 +0200 Hi, Last week another user reported very similar problems (also 164% deviations, I think). In that case it seemed that the user did an Angstrom to nm conversion in the table file on x without scaling f(x). Could this also be your issue? Berk From: xiaowu...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] a bit strange errors Date: Fri, 16 Oct 2009 14:55:40 +0800 Dear Mark, Thank you very much for the quick reply to my post. According to your suggestion, I check the table and reformat it with equal spacing between entries. I also check the entries calculated from the analytical functions and no wrong values are found. However, the same warnings are given, which lead to terminate the simulation. Are there any other reasons responsible for it? Best wishes, Chaofu Wu, Dr. > Date: Fri, 16 Oct 2009 14:18:17 +1100 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] a bit strange errors > > wuxiao wrote: > > Dear GMXers, > > Recently, I has been performing coarse-grained MD simulations based > > on the tabulated potentials using GROMACS. In the initialization, some > > warnings are given as follows > > /WARNING: For the 999 non-zero entries for table 0 in table_b0.xvg the > > forces deviate on average 164% from minus the numerical derivative of > > the potential/ > > This looks like your table has either wrong values or wrong formatting. > It does have to have equal spacing between entries. > > > It proceeds untill at about 17 ns before it is interupted with some errors > > /WARNING: 1-4 interaction between 148 and 151 at distance 13.125 which > > > > is larger than the 1-4 table size 2.000 nm/ > > I think the duartion time is long enough to equilibrated the system, > > which is confirmed by the energy plot with time. Why it happens so? What > > should I do to cope with this problem? Thanks a lot for any reply to > > Perhaps much of the table is fine, and the problem only arises when you > get a force being looked up in an erroneous part. > > Mark > ___ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php 使用新一代 Windows L iv e Messenger 轻松交流和共享！ 立刻下载！ What can you do with the new Windows Live? Find out 更多热辣资讯尽在新版MSN首页！ 立刻访问！ _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] a bit strange errors
Dear Berk, Unfortunately, this time it is angle (table_a0.xvg) that cause the problem. The angles are taken in degrees. I think it is not due to the wrong unit. Anyway, thanks very much for your reply. Best wishes, Chaofu Wu, Dr. From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] a bit strange errors Date: Fri, 16 Oct 2009 09:21:18 +0200 Hi, Last week another user reported very similar problems (also 164% deviations, I think). In that case it seemed that the user did an Angstrom to nm conversion in the table file on x without scaling f(x). Could this also be your issue? Berk From: xiaowu...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] a bit strange errors Date: Fri, 16 Oct 2009 14:55:40 +0800 Dear Mark, Thank you very much for the quick reply to my post. According to your suggestion, I check the table and reformat it with equal spacing between entries. I also check the entries calculated from the analytical functions and no wrong values are found. However, the same warnings are given, which lead to terminate the simulation. Are there any other reasons responsible for it? Best wishes, Chaofu Wu, Dr. > Date: Fri, 16 Oct 2009 14:18:17 +1100 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] a bit strange errors > > wuxiao wrote: > > Dear GMXers, > > Recently, I has been performing coarse-grained MD simulations based > > on the tabulated potentials using GROMACS. In the initialization, some > > warnings are given as follows > > /WARNING: For the 999 non-zero entries for table 0 in table_b0.xvg the > > forces deviate on average 164% from minus the numerical derivative of > > the potential/ > > This looks like your table has either wrong values or wrong formatting. > It does have to have equal spacing between entries. > > > It proceeds untill at about 17 ns before it is interupted with some errors > > /WARNING: 1-4 interaction between 148 and 151 at distance 13.125 which > > > > is larger than the 1-4 table size 2.000 nm/ > > I think the duartion time is long enough to equilibrated the system, > > which is confirmed by the energy plot with time. Why it happens so? What > > should I do to cope with this problem? Thanks a lot for any reply to > > Perhaps much of the table is fine, and the problem only arises when you > get a force being looked up in an erroneous part. > > Mark > ___ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php 使用新一代 Windows L iv e Messenger 轻松交流和共享！ 立刻下载！ What can you do with the new Windows Live? Find out _ 约会说不清地方？来试试微软地图最新msn互动功能！ http://ditu.live.com/?form=TL&swm=1___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] a bit strange errors
Hi, Last week another user reported very similar problems (also 164% deviations, I think). In that case it seemed that the user did an Angstrom to nm conversion in the table file on x without scaling f(x). Could this also be your issue? Berk From: xiaowu...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] a bit strange errors Date: Fri, 16 Oct 2009 14:55:40 +0800 Dear Mark, Thank you very much for the quick reply to my post. According to your suggestion, I check the table and reformat it with equal spacing between entries. I also check the entries calculated from the analytical functions and no wrong values are found. However, the same warnings are given, which lead to terminate the simulation. Are there any other reasons responsible for it? Best wishes, Chaofu Wu, Dr. > Date: Fri, 16 Oct 2009 14:18:17 +1100 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] a bit strange errors > > wuxiao wrote: > > Dear GMXers, > > Recently, I has been performing coarse-grained MD simulations based > > on the tabulated potentials using GROMACS. In the initialization, some > > warnings are given as follows > > /WARNING: For the 999 non-zero entries for table 0 in table_b0.xvg the > > forces deviate on average 164% from minus the numerical derivative of > > the potential/ > > This looks like your table has either wrong values or wrong formatting. > It does have to have equal spacing between entries. > > > It proceeds untill at about 17 ns before it is interupted with some errors > > /WARNING: 1-4 interaction between 148 and 151 at distance 13.125 which > > > > is larger than the 1-4 table size 2.000 nm/ > > I think the duartion time is long enough to equilibrated the system, > > which is confirmed by the energy plot with time. Why it happens so? What > > should I do to cope with this problem? Thanks a lot for any reply to > > Perhaps much of the table is fine, and the problem only arises when you > get a force being looked up in an erroneous part. > > Mark > ___ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php 使用新一代 Windows Liv e Messenger 轻松交流和共享！ 立刻下载！ _ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
