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 check my uncompleated system ). As I understood One of the possible way is the ussage of G_energy but how I could obtain GRO and TPR file from uncompleated MD trajectory ( .trr) (recently I've asked about this but I've missed that topic ;o) ? Thanks again James 2011/11/25 Tsjerk Wassenaar <tsje...@gmail.com> > 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" <jmsstarli...@gmail.com> 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). > > Because my peptide was smaller than typical globular protein I've desided > to use bigger periodical box than in tutorial > > I've used editconf -c -d 1.5 -bt cubic instead of 1.0 nm in tutorial wich > resulted in bigger box relative peptide size. > > so i have this box vectors 5.39318 5.39318 5.39318 > > My experiment was in full agreement with the above tutorial until NVP > phase was conducted. I have conducted 100ps equilibration but When I've > checked average pressure it was 0.75 atm instead of 1 BAR and have big > RMSD- 200. (also I've checked my system visually but it looks fine- I have > not pointed any artifacts linked with unstable pressure like voids in the > solvent etc). Should I equilibrate my sustem longer until pressure would > not be stabilized to reference BAR? What another options should i take > into account during simulation of the small peptides ? > > Thanks, > > James > > -- > 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 >
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