Re: [gmx-users] Doubt about the Gromacs versions

Thanks for your reply. On Thu, Apr 25, 2013 at 7:18 PM, Richard Broadbent < richard.broadben...@imperial.ac.uk> wrote: > The 4.6.1 release is a more advanced version of gromacs with the latest > kernels and features (GPU support, verlet cut-offs etc.). > > 4.5.7 is a maintenance release for thos

Re: [gmx-users] Doubt about the Gromacs versions

Thanks for the clarification. On Thu, Apr 25, 2013 at 7:48 PM, Justin Lemkul wrote: > > > On 4/25/13 9:48 AM, Richard Broadbent wrote: > >> The 4.6.1 release is a more advanced version of gromacs with the latest >> kernels >> and features (GPU support, verlet cut-offs etc.). >> >> 4.5.7 is a ma

Re: [gmx-users] Re: Martini with PME, temp two low (ABEL Stephane 175950)

Good. Note however that we do get the right temperature with a dt=20fs with Martini so you energy leak might be in the cutoff scheme or the system is really badly equilibrated. On Apr 25, 2013, at 18:23, ABEL Stephane 175950 wrote: > Xavier > > I have followed your suggestion and did a lon

Re: [gmx-users] Re: Manual installation of new analysis tool

Dear Mark & Junghans, Thanks for your valuable suggestions. I have gone through the README file. It says compatibility with 4.5.x version. I am using 4.5.5. So, I think its not a problem. @Junghans: I have installed pkg-config in fact the $ pkg-config --libs libgmx returns the expected output;

Re: [gmx-users] RMSD from the average structure

Thanks for your reply. Actually I am interested to see how much structural deviation is occurring in a protein during the simulation from its average position of atoms rather than the initial position (crystal structure or starting structure). The motivation of doing this analysis is the fact that

[gmx-users] Re: Manual installation of new analysis tool

> Date: Thu, 25 Apr 2013 22:57:55 +0200 > From: Mark Abraham > Subject: Re: [gmx-users] Manual installation of new analysis tool > To: Discussion list for GROMACS users > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > On Wed, Apr 24, 2013 at 8:14 AM, Venkat Reddy wrote

Re: [gmx-users] issue in replica exchange

Thanks for the answer. I'll check gmx4.5.7 and report back. I am not sure what you mean by GROMACS swaps the coordinates not the ensemble data. The coupling to P and T and not exchanged with it? That would explain what I see, but let see what 4.5.7 has to say first. Tks. On Apr 25, 2013, a

Re: [gmx-users] Manual installation of new analysis tool

On Wed, Apr 24, 2013 at 8:14 AM, Venkat Reddy wrote: > Dear all, > I have got an analysis tool for analyzing membrane density from Dr.Luca > monticelli. I have followed the installation instructions as given. > > 1) First thing is to load GROMACS >$ *source /usr/local/gromacs/bin/GMXRC* > 2)

Re: [gmx-users] Fwd: amber03 force field

X-C-CN-X is not present in amber03 in the GROMACS distribution. You seem to be using some modified version. Please ask the person who modified it :-) Mark On Wed, Apr 24, 2013 at 4:26 PM, Elisa Frezza wrote: > Dear All, > > I am starting to use amber03 force field, but I have found something ve

Re: [gmx-users] Fwd: Selecting the temperature distribution

Yes, I got exchanges. By construction! :-) Email me off-list if you would like a methods description (for what it is worth). Mark On Thu, Apr 25, 2013 at 1:11 PM, massimo sandal wrote: > This hints at an interesting protocol/attempt, at least for a sort of > newbie like me. Can you elaborate?

Re: [gmx-users] issue in replica exchange

Thanks for the good report. There have been some known issues about the timing of coupling stages with respect to various intervals between GROMACS events for some algorithms. There are a lot of fixed problems in 4.5.7 that are not specific to REMD, but I have a few lingering doubts about whether w

Re: [gmx-users] RMSD from the average structure

Hi Bipin Singh, That indeed gives you the RMSD against the average. Do think about it a bit more: do you want the average of the whole structure, or should you account for a phase of relaxation? Cheers, Tsjerk On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul wrote: > > > On 4/24/13 3:06 AM, bi

[gmx-users] How to rescue trr trajectory when two or more corrupted frames exist

Dear Gromacs users, I have some corrupted frames in different trajectories. gmxcheck with .trr trajectories gives extraordinary positions or velocities and with .xtc trajectories gives rise to the magic number error. I am aware of the program gmx_rescue kindly offered to us by its developers. H

Re: [gmx-users] Problem with gromacs in Cluster

This works well until you use a system that permits job suspension. Then -maxh gets double-crossed... :-) Mark On Apr 25, 2013 3:41 PM, "Richard Broadbent" < richard.broadben...@imperial.ac.uk> wrote: > I generally build a tpr for the whole simulation then submit one job using > a command such as

Re: [gmx-users] free energy of system

On 4/25/13 12:02 PM, sarah k wrote: Dear all, I'm interested in calculating the Gibbs free energy of some systems. I have several questions in this regard: 1- The g_energy command gives some values in kJ/mol for total energy and enthalpy. Does the reported total energy include entropy effects

[gmx-users] Re: Martini with PME, temp two low (ABEL Stephane 175950)

Xavier I have followed your suggestion and did a longer NPT equilibration with smaller dt and ntlist values and It works. The Energy and Temp reach to stables values as i want. thank you again for your help Stephane -- Message: 2 Date: Thu, 25 Apr 2013 14:17:

[gmx-users] free energy of system

Dear all, I'm interested in calculating the Gibbs free energy of some systems. I have several questions in this regard: 1- The g_energy command gives some values in kJ/mol for total energy and enthalpy. Does the reported total energy include entropy effects? (The calculated total energy and entha

[gmx-users] Re: How to use multiple nodes, each with 2 CPUs and 3 GPUs

Dear Szilárd: Thank you for your assistance. I understand the importance of reading the documentation and I read it about 5 times before I posted to this list. In fact, it's kind of buried in my initial post, but I did run MPI gromacs with mpirun -np 3 the first time and it didn't work. I have

Re: [gmx-users] How to use multiple nodes, each with 2 CPUs and 3 GPUs

Hi, You should really check out the documentation on how to use mdrun 4.6: http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Running_simulations Brief summary: when running on GPUs every domain is assigned to a set of CPU cores and a GPU, hence you need to start as many PP MPI

[gmx-users] interfacial-tension-interface simulation

Dear Gromacs users, I'm simulating a water-oil interface. From litterature interfacial tension is determined from pressure tensors as follows:1/2 (Pz - (px+py)/2))*Lz Where Pz, Px and Py are the pressure tensors in the different axis. I did a NPT simulation step and I want to check my interfacial

Re: [gmx-users] How to fix interfacial tension in NPT

Thank you for your reply :) I will look further On 25 April 2013 23:18, Justin Lemkul wrote: > > > On 4/25/13 9:10 AM, Souilem Safa wrote: > >> Dear Justin, >> Please I want to ask you for the calculation of interfacial tension from >> the formula : 1/2 (Pz - (px+py)/2))*Lz >> Should I calculat

[gmx-users] How to use multiple nodes, each with 2 CPUs and 3 GPUs

Thank you Berk, I am still getting an error when I try with MPI compiled gromacs 4.6.1 and -np set as you suggested. I ran like this: mpirun -np 6 /nics/b/home/cneale/exe/gromacs-4.6.1_cuda/exec2/bin/mdrun_mpi -notunepme -deffnm md3 -dlb yes -npme -1 -cpt 60 -maxh 0.1 -cpi md3.cpt -nsteps 5000

Re: [gmx-users] g_rmsf Analysis.

On 4/25/13 10:12 AM, Vivek Modi wrote: Hello, I am using g_rmsf for analysis of a protein simulation. I want to calculate the fluctuations with respect to a reference structure (using -od option). But I am encountering a problem. Please correct me if I am wrong at some place. The following two

Re: [gmx-users] How to fix interfacial tension in NPT

On 4/25/13 9:10 AM, Souilem Safa wrote: Dear Justin, Please I want to ask you for the calculation of interfacial tension from the formula : 1/2 (Pz - (px+py)/2))*Lz Should I calculate the interfacial tension in every step and take the average interfacial tension for all the steps or should I ta

Re: [gmx-users] Doubt about the Gromacs versions

On 4/25/13 9:48 AM, Richard Broadbent wrote: The 4.6.1 release is a more advanced version of gromacs with the latest kernels and features (GPU support, verlet cut-offs etc.). 4.5.7 is a maintenance release for those of us who for whatever reason wish to keep using the older 4.5.x series releas

Re: [gmx-users] Martini with PME, temp two low

On 4/25/13 10:05 AM, Dr. Vitaly Chaban wrote: PME should NOT be used with charged systems, for obvious reasons. FYI Gromacs provides a neutralizing background charge. http://comments.gmane.org/gmane.science.biology.gromacs.user/639 There may, of course, be issues with the physical reality

[gmx-users] Re: Martini with PME, temp two low

@ Vitaly of course. I know that. My system is neutral but with charged particles (AOT and Na+). @Xavier I will try your suggestion and equilibrate my system for a longer period Thanks again Stephane -- Message: 1 Date:

[gmx-users] g_rmsf Analysis.

Hello, I am using g_rmsf for analysis of a protein simulation. I want to calculate the fluctuations with respect to a reference structure (using -od option). But I am encountering a problem. Please correct me if I am wrong at some place. The following two methods are giving me different results. I

Re: [gmx-users] Martini with PME, temp two low

PME should NOT be used with charged systems, for obvious reasons. On Thu, Apr 25, 2013 at 4:00 PM, ABEL Stephane 175950 wrote: > And ? sorry but i do not understand... > > Stephane > > -- > > Message: 2 > Date: Thu, 25 Apr 2013 15:39:12 +0200 > From: "Dr. Vitaly Chaba

[gmx-users] Martini with PME, temp two low

And ? sorry but i do not understand... Stephane -- Message: 2 Date: Thu, 25 Apr 2013 15:39:12 +0200 From: "Dr. Vitaly Chaban" Subject: Re: [gmx-users] Martini with PME, temp two low To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain;

[gmx-users] sc-coul and sc-r-power

Hello, My simulations crash when using sc-r-power 48, even if I'm running with sc-coul = no, couple_lambda0 = vdw-q couple_lambda1 = vdw. If I'm running couple_lambda0 = vdw and couple_lambda1 = none it works. The fe config that is causing a crash is: init_lambda-state = 0 couple-intramol

Re: [gmx-users] Martini with PME, temp two low

Well … 400 ps is rather small and you can expect deviations from so short simulations if you start from an non-equilibrated system. I am not sure what the void is but this indicates that your system might not be equilibrated … You can try to decrease the time step and nstlist to see if you the

Re: [gmx-users] Doubt about the Gromacs versions

The 4.6.1 release is a more advanced version of gromacs with the latest kernels and features (GPU support, verlet cut-offs etc.). 4.5.7 is a maintenance release for those of us who for whatever reason wish to keep using the older 4.5.x series release. It mainly adds fixes made to the 4.6.x ser

Re: [gmx-users] Problem with gromacs in Cluster

The salvation is to use: mdrun -cpi state.cpt Dr. Vitaly Chaban On Thu, Apr 25, 2013 at 2:37 PM, Justin Lemkul wrote: > > >> Can any body tell me how do it split script i such that i will get all >> 20ns simulation >> >> > You specified a given time limit for the job, and the run exceede

Re: [gmx-users] Martini with PME, temp two low

Sorry for the double post, but i forgot to remove the others message. I have also added the average values obtained for this run Statistics over 20001 steps using 4001 frames Energies (kJ/mol) Bond G96AngleLJ (SR) Coulomb (SR) Coul. recip. 1.65683e+04

Re: [gmx-users] Problem with gromacs in Cluster

I generally build a tpr for the whole simulation then submit one job using a command such as: mpirun -n ${NUM_PROCESSORS} mdrun -deffnm ${NAME} -maxh ${WALL_TIME_IN_HOURS} copy all the files back at the end of the script if necessary then: then resubmit it (sending out all the files again if

Re: [gmx-users] Martini with PME, temp two low

Hmmm Aren't the keywords here "charged system" + "PME"? Dr. Vitaly Chaban On Thu, Apr 25, 2013 at 1:34 PM, XAvier Periole wrote: > > Did you visualise the system? T in function of time? Epot in function of > time? > > As a side note (not relevant for PME) the mix of nstlist = 10 and the

[gmx-users] Doubt about the Gromacs versions

Hi, Please let me know which one is the recent version of gromacs (with latest bugfixes) among the below. 4.5.7 and 4.6.1 And what is the reason behind the update for 4.5.x versions if 4.6.x versions are already available. -- *--- Thanks and Regards, Bipin Singh* -- gmx-use

[gmx-users] RE : gmx-users Digest, Vol 108, Issue 154

Hello Xavier, Thank you for your response. >> nstlist = 10 and the rlist = 1.0 My mistake, i did not changes these values when i switched to PME, I have rerun the simulations for 400 ps in NPT with these changes and plotted Epot and Temp vs Time The Epot and Temp values are not stables. The

Re: [gmx-users] How to fix interfacial tension in NPT

Dear Justin, Please I want to ask you for the calculation of interfacial tension from the formula : 1/2 (Pz - (px+py)/2))*Lz Should I calculate the interfacial tension in every step and take the average interfacial tension for all the steps or should I take the average of the presssure tensors from

Re: [gmx-users] Problem with gromacs in Cluster

You can split the simulation in different part (for example 5 ns each), every time you'll finish one you will extend it adding more time. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations?highlight=extend My cluster uses a different "script system" than yours so I can't help with

Re: [gmx-users] Problem with gromacs in Cluster

On 4/25/13 8:28 AM, Sainitin Donakonda wrote: Hey all, I recently ran 20ns simulation of protein ligand complex on cluster i used following script to run simulation grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_test.tpr mpirun -n 8 mdrun -s md_test.tpr -deffnm md_tes

[gmx-users] Problem with gromacs in Cluster

Hey all, I recently ran 20ns simulation of protein ligand complex on cluster i used following script to run simulation grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_test.tpr mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8 *I saved this as MD.sh And then submited

RE: [gmx-users] Differences between 4.5.5 and 4.6.2-dev?

Hi, Twin-range will lead to extra errors, which could be negligible or not. But the errors should be the same and have the same effects in different versions. I think nothing has changed in the twin-range treatment from 4.5 to 4.6, but I am not 100% sure. Which version with twin-range matches y

Re: [gmx-users] Martini with PME, temp two low

Did you visualise the system? T in function of time? Epot in function of time? As a side note (not relevant for PME) the mix of nstlist = 10 and the rlist = 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and rlist=1.4 if nstlist =10. On Apr 25, 2013, at 1:10 PM, ABEL Stephane 1

[gmx-users] issue in replica exchange

Hi, I have been recently using the REMD code in gmx-407 and gmx-453 and got a few systems crashing for unclear reasons so far. The main tests I made are using gmx407 but it is all reproducible with gmx453. The crashing was also reproduced (not necessarily at the same time point) on several arc

[gmx-users] Martini with PME, temp two low

Hello all, I am trying to test the martini force field with PME for a charged system that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. My system works well, if i use the standard shift parameters (correct temp, and pressure). But for for the simulation with PME , the

Re: [gmx-users] Fwd: Selecting the temperature distribution

This hints at an interesting protocol/attempt, at least for a sort of newbie like me. Can you elaborate? Did they exchange? On 25 Apr 2013 13:06, "Mark Abraham" wrote: > Likewise, I agreed with what Massimo said. > > As an example, I recently did a fairly large set of REMD simulations of a > 320-

Re: [gmx-users] Fwd: Selecting the temperature distribution

Likewise, I agreed with what Massimo said. As an example, I recently did a fairly large set of REMD simulations of a 320-atom disordered peptide with rather more water and many fewer replicas than you propose. I did so because I expected low barriers and large maximum diameter (the latter from an

Re: [gmx-users] Differences between 4.5.5 and 4.6.2-dev?

Dear Berk, der GMXers, On Apr 23, 2013, at 2:54 PM, Stefan Kesselheim wrote: > The temperature is 300.6, target temperature was 300. That should be fine. I > did check weaker fields and weaker thermostat coupling. Everything stayed > optimally consistent, within 4.5.5, however incompatible wi

RE: [gmx-users] How to use multiple nodes, each with 2 CPUs and 3 GPUs

Hi, You're using thread-MPI, but you should compile with MPI. And then start as many processes as total GPUs. Cheers, Berk > From: chris.ne...@mail.utoronto.ca > To: gmx-users@gromacs.org > Date: Wed, 24 Apr 2013 17:08:28 + > Subject: [gmx-users] How to use multiple nodes, each with 2 CPUs