Re: [gmx-users] Brownian Dynamics Simulations generating huge log files

I set nstlog = 1000, and still I get a 5MB log file within a minute of starting the sim. It seems absurd, but its happening :( On Thu, Dec 16, 2010 at 10:05 AM, Justin A. Lemkul wrote: > > > Nimesh Jain wrote: > >> Hi, >> >> I am trying to simulate

[gmx-users] Brownian Dynamics Simulations generating huge log files

Hi, I am trying to simulate a system of 880 particles with implicit solvent using brownian dynamics, but the simulation generates huge log files (it writes md.log files at a rate of almost 5MB/minute) and this crashed my system since I ran out of space :( My mdp file looks like this: include

[gmx-users] RE: Log files

How do I turn off md.log fine generation in Gromacs? Thanks -- gmx-users mailing listgmx-users@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 requ

[gmx-users] RE: Temperature Fluctuations

Hi, I am doing Replica Exchange (RE) simulations with 8 replicas 10 degree apart. My system has implicit solvent and there is only one molecule in the system (around 270 atoms). I am using Nose-Hover thermostat and tabulated potentials. When I do simulations with exchange frequency of 1 ns, the sy

Re: [gmx-users] RE: gro file and topology files

! On Tue, Nov 9, 2010 at 12:37 PM, Justin A. Lemkul wrote: > > > Nimesh Jain wrote: > >> Hi, >> >> I was wondering if the order of molecules in topology file and the order >> of coordinates in gro file have to be same. My files are as follows: >> >>

[gmx-users] RE: gro file and topology files

Hi, I was wondering if the order of molecules in topology file and the order of coordinates in gro file have to be same. My files are as follows: gro file: 1624 1B1 C1 22.237 30.408 26.522 1B1 SA2 22.348 30.033 26.829 1B1 P3 22.125 30.102 27.144

[gmx-users] RE: Error in mdrun

Hi, I keep getting the following error when I do mdrun: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or

[gmx-users] Restart Replica Exchange

Hi, I was wondering if anyone knows whether it is possible to restart a replica exchange simulation if it stops during the run. I tried it once before and got the error that all the replicas should be at the same time step for replica exchange. When I checked the time step of different replicas, t

[gmx-users] RE: Molecule out of pbc box

Hi, Does anyone know if there is a way to put a molecule back in the pbc box in gromacs. I am visualizing my sims in vmd and the molecule keeps going out of the box. Is it normal or an artifact in vmd, is there a way to put the molecule back in the box? please let me know. Thanks, Nimesh -- gmx-

[gmx-users] RE: Targeted MD

Hello, I realize that this topic has been discussed before, but I just need to ascertain a few things: I have a system of about 1400 atoms with implicit solvent and I want to do a targeted MD. While doing the pre-processing, if I just specify "grompp -r in.gro -rb out.gro", is this sufficient or a

Re: [gmx-users] RE: log files

log file as > 'nstlog = 10'. > Given that 'nsteps = 1', you're writing to the > log file only 1000 times. Do you get a 20GB md.log file with these settings? > > -Gaurav > > On Wed, Aug 11, 2010 at 10:52

[gmx-users] RE: log files

Hi, I am having some problem in my simulations related to log files. The file sizes are enormous, its like after 3 days of simulation I had a 20 GB md.log file. One of my grompps looks like this: [tau_t is very low because I am using bd and it doesn't work otherwise]. [I am doing a replica exchang

Re: [gmx-users] Problem in Replica Exchange

. All suggestions were really helpful. Thanks, Nimesh On Tue, Aug 3, 2010 at 10:23 AM, David van der Spoel wrote: > On 2010-08-03 17.17, Nimesh Jain wrote: > >> And the simulation is for 100ns. >> > So you are trying exchanges ecery 2 ns (assuming 2 fs timestep). That is > rathe

Re: [gmx-users] Problem in Replica Exchange

And the simulation is for 100ns. On Tue, Aug 3, 2010 at 10:17 AM, Nimesh Jain < nimeshjain2...@u.northwestern.edu> wrote: > mdrun command I am using: (I have a shell script that adds jobs on the > server) Following are the contents of that: > > #!/bin/bash > # > #$ -cw

Re: [gmx-users] Problem in Replica Exchange

ile $PWD/machines \ /share/apps/gromacs-4.0.5/bin/mdrun_mpi \ -s topol_.tpr -multi 8 -pd replex 100 Thanks, Nimesh On Tue, Aug 3, 2010 at 10:11 AM, David van der Spoel wrote: > On 2010-08-03 17.08, Nimesh Jain wrote: > >> Hi, >> >> I am doing a replica

[gmx-users] Problem in Replica Exchange

Hi, I am doing a replica exchange simulation with 8 replicas. I was looking at my data and I observed that a couple of replicas are around 10 and 20 ns ahead of everything else. Is it normal or is this wrong ? Please let me know. Thanks, Nimesh -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Free Energy Calculation Using Tabulated Potentials

Hi, I am having some troubles calculating free energies. Can someone please tell me if I have tabulated potentials, can I calculate free energy using the gromacs options in the mdp file for free energies. (If someone has done it, can you please provide a sample topology file.) Thanks, Nimesh -