HI Maggin, The Pressure came from NPT simulation, I apologize for the lack of annotation. Here are some of the outputs of your suggested checks of equilibrium https://docs.google.com/spreadsheet/ccc?key=0Ao2bINpUakZ-dHpiZG9SOXhkX0JGNXlqTHBfQ1kwbnc&usp=sharing
I'm currently looking into the rvdw value as you suggested as well as the fourierspacing as Mark suggested. However to help with this problem I've uploaded all of .mdp files as well as my bash script here -> https://gist.github.com/ParkerdeWaal/8a7a73682e04a4878902 Maybe there is a problem with my choice of box size? -bt cubic -d 1? Viewing the boxed and solvated system showed a distance of ~10A between the protein and the box which should be ample. Additionally a full output log of the run can be found here -> http://research.parkerdewaal.com/slurm-940372.out which seems to be error free until the final md run. Thanks Everyone, Parker On Fri, Jun 14, 2013 at 9:56 AM, maggin <maggin.c...@gmail.com> wrote: > Hi, Parker, > > gromos53a6 force field, rvdw=1, if it right ? please check. > > Your ref_p = 1.0, So, Pressure average of 1.9 is come from which step? NVT, > NPT, md ? > > Actually, we use: g_energy -f npt.edr -o pressure.xvg > to see if NPT has reached equilibrium. > > g_energy -f nvt.edr > to see if NVT has reached equilibrium. > > maggin > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/System-equilibrium-problems-tp5009137p5009157.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
