Re: [gmx-users] Pressure stabilization during NPT phase

On 25/11/2011 6:53 PM, James Starlight wrote: This way I've already used but is this possible to extract Gro and trp files from uncompleated runs and not stopping this simulation ? Copy the trajectory file. Then use trjconv on the copy however suits you. You don't need a new .tpr, you need

Re: [gmx-users] Pressure stabilization during NPT phase

Hey, You don't actually need to copy the trajectory. trjconv and other tools are comfortable operating on an unfinished trajectory. They'll just bail out at the end. As an alternative, here's a python one-liner to extract the last frame (along with unfinished frames) from an XTC trajectory:

Re: [gmx-users] Pressure stabilization during NPT phase

Oh, I see I forgot to state that X should be set to the trajectory name: X=/some/where/trajectory.xtc python -c 'X=open('$X').read(); print X[X.rfind(X[:8]):]' last.xtc or just python -c 'X=open(/some/where/trajectory.xtc).read(); print X[X.rfind(X[:8]):]' last.xtc Cheers, Tsjerk On Fri,

[gmx-users] Pressure stabilization during NPT phase

Dear Gromacs Users! At the present time I'm simulating small peptide (11 a.c in coiled conformation) in water. I've desided to use parameters from Lysozyme simmulation ( opls ff for parametrisation and all mdp parameters from that simulation). Because my peptide was smaller than typical

Re: [gmx-users] Pressure stabilization during NPT phase

On 25/11/2011 5:22 PM, James Starlight wrote: Dear Gromacs Users! At the present time I'm simulating small peptide (11 a.c in coiled conformation) in water. I've desided to use parameters from Lysozyme simmulation ( opls ff for parametrisation and all mdp parameters from that simulation).

Re: [gmx-users] Pressure stabilization during NPT phase

Hi James, There have been extensive discussions about this on the list. Check the archives. In short, smaller systems give larger fluctuations, and shorter simulations give larger deviations from the expected average. Cheers, Tsjerk On Nov 25, 2011 7:23 AM, James Starlight

Re: [gmx-users] Pressure stabilization during NPT phase

Mark, Tsjerk thanks! I've check my uncompleated produced MD run by G_energy and find that average pressure is 1.1 Bar that is most close to ref. By the way could you tell me about extra possible ways of checking running simmulation? ( E.g I'm calculating long produce trajectory and want to

Re: [gmx-users] Pressure stabilization during NPT phase

On 25/11/2011 6:38 PM, James Starlight wrote: Mark, Tsjerk thanks! I've check my uncompleated produced MD run by G_energy and find that average pressure is 1.1 Bar that is most close to ref. By the way could you tell me about extra possible ways of checking running simmulation? ( E.g I'm

Re: [gmx-users] Pressure stabilization during NPT phase

This way I've already used but is this possible to extract Gro and trp files from uncompleated runs and not stopping this simulation ? James 2011/11/25 Mark Abraham mark.abra...@anu.edu.au On 25/11/2011 6:38 PM, James Starlight wrote: Mark, Tsjerk thanks! I've check my uncompleated