Hi, I am fairly new to simulation, and would like some input about whether I have set up Gromacs correcly. I am using version 5.0.4 with the CHARMM36-Jun2015 force field and the TIP3P water model. I am simulating a 35kDa protein in a dodecahedron box (-d 1.6) with 150mM NaCl plus neutralizing ions.
I do a 200ps NVT equilibration followed by a 500ps NPT equilibration followed by 230ps of production run where the protein is unrestrained. My observations so far are that the density is higher than I would expect from reading literature. I would appreciate any insight into whether I have a problem, or if my density and pressure values look acceptable. Thanks in advance Here are my results from gmx energy: *Energy minimization* Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Potential -1.93229e+06 29000 77735.5 -189748 (kJ/mol) *NVT Equilibration 200ps* Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Temperature 299.9 0.099 2.59846 0.560458 (K) *NPT Equilibration 500ps* Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Pressure 1.52892 1.7 81.0079 11.2974 (bar) Density 1024.74 0.057 1.70907 -0.0499058 (kg/m^3) Volume 1168.76 0.065 1.96293 0.0505822 (nm^3) *Production Run 230ps* Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Pressure 0.450022 0.65 75.3012 0.157248 (bar) Density 1025.4 0.048 1.39937 -0.209504 (kg/m^3) Volume 1168.01 0.055 1.59374 0.238338 (nm^3) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.