Re: [gmx-users] Extending Simulations

On 6/26/13 4:12 PM, HANNIBAL LECTER wrote: It is not very clear as to what you are trying to do? If you have the final coordinates and velocities from a previous simulation, I would recommend start a simulation using the .gro file and ensuring that you have gen-vel=no in the .mdp file. If you

Re: [gmx-users] Extending Simulations

It is not very clear as to what you are trying to do? If you have the final coordinates and velocities from a previous simulation, I would recommend start a simulation using the .gro file and ensuring that you have gen-vel=no in the .mdp file. If you have a well-equilibrated system, then the prope

[gmx-users] Extending Simulations

Hi everybody, I have a question that relates to reproducibility in Gromacs. If I have a .cpt file from a previous simulation and use that for two simulations using tpbconv, how similar should the temperature graphs etc be? When I use the .edr files to plot various properties, there is significant

Re: [gmx-users] extending simulations made with version 3.3.3

On 11/12/2010 2:19 AM, Anna Marabotti wrote: Dear all, I conserved all the files produced sometimes ago with a simulation made with Gromacs 3.3.3 installed on a cluster. I would like to prolonge this simulation, but I have no longer access to that cluster, instead I can access another cluster

[gmx-users] extending simulations made with version 3.3.3

Dear all, I conserved all the files produced sometimes ago with a simulation made with Gromacs 3.3.3 installed on a cluster. I would like to prolonge this simulation, but I have no longer access to that cluster, instead I can access another cluster with Gromacs 4.0.X installed. What are the risks o

Re: [gmx-users] Extending simulations

Milan Melichercik wrote: On Wednesday 17 March 2010 13:53:03 Carla Jamous wrote: Hi everyone, It's the first I use the process of extending simulations. I did the following: tpbconv -s prot.tpr -extend 6000 -o protein.tpr mdrun -v -s protein.tpr -cpi state.cpt -cpo state_a.cpt -o protein.trr

Re: [gmx-users] Extending simulations

On Wednesday 17 March 2010 13:53:03 Carla Jamous wrote: > Hi everyone, > > It's the first I use the process of extending simulations. > I did the following: > tpbconv -s prot.tpr -extend 6000 -o protein.tpr > > mdrun -v -s protein.tpr -cpi state.cpt -cpo state_a.cpt -o protein.trr -c > protein.gr

[gmx-users] Extending simulations

Hi everyone, It's the first I use the process of extending simulations. I did the following: tpbconv -s prot.tpr -extend 6000 -o protein.tpr mdrun -v -s protein.tpr -cpi state.cpt -cpo state_a.cpt -o protein.trr -c protein.gro -x protein.xtc -e md.edr -g md.log But I noticed sthg strange: gromac

Re: [gmx-users] extending simulations

acs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Anna Marabotti >> Sent: Wednesday, May 06, 2009 8:31 AM >> To: gmx-users@gromacs.org >> Subject: [gmx-users] extending simulations >> >> Dear all, >> I'd need to have a clarification about

Re: [gmx-users] extending simulations

file i am waiting for your reply thanks in Advance --- On *Wed, 6/5/09, kyungchan chae //* wrote: From: kyungchan chae Subject: RE: [gmx-users] extending simulations To: "'Discussion list for GROMACS users'" Date: Wednesday, 6 May,

RE: [gmx-users] extending simulations

: No such file or directory  please kindly rectify the error in the configure file i am waiting for  your reply thanks in Advance                   --- On Wed, 6/5/09, kyungchan chae wrote: From: kyungchan chae Subject: RE: [gmx-users] extending simulations To: "'Discussion list f

RE: [gmx-users] extending simulations

ailto:gmx-users-boun...@gromacs.org] On Behalf Of Anna Marabotti Sent: Wednesday, May 06, 2009 8:31 AM To: gmx-users@gromacs.org Subject: [gmx-users] extending simulations Dear all, I'd need to have a clarification about how to extend a simulation made using GROMACS 4 that has been interrupted on

Re: [gmx-users] extending simulations

Anna Marabotti wrote: Dear all, I'd need to have a clarification about how to extend a simulation made using GROMACS 4 that has been interrupted on a system due to walltime expiration. On the Wiki section I see: "A simulation that has completed is extended using tpbconv, mdrun and checkpoint

Re:[gmx-users] extending simulations

You can use the mdrun command: How to restart a crashed run. The mdrun program now uses a very handy checkpointing feature. Restarting crashed runs is easy with mdrun. mdrun -s prev.tpr -f prev.trr -e prev.edr -o prev.trr –g prev.log –cpi -append 在2009-05-06，"Anna Marabotti" 写道： >Dear al

[gmx-users] extending simulations

Dear all, I'd need to have a clarification about how to extend a simulation made using GROMACS 4 that has been interrupted on a system due to walltime expiration. On the Wiki section I see: "A simulation that has completed is extended using tpbconv, mdrun and checkpoint files (.cpt). A simulation