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
