Dear gromacs users, I know similar issues have been raised many times on the list but I am unable to solve the problem so I am seeking your advice. I am trying to simulate a protein in a dodecahedron box. The system size is ~30k atoms. I have followed the methodology given in the lysozyme tutorial i.e. minimization, nvt, npt and production. However the average pressure values after 5, 10, 20 ns of npt equilibration are not coming close to the reference pressure i.e 1 bar when using parrinello rahman. I checked the mailing list and tried using Berendson and after 10 ns I get average pressure close to 1 (0.85). However when I switch to parrinello rahman for production run the average pressure again goes far from 1. Can someone please help me with this? Here are the g_energy outputs from equilibration (parrinello rahman, 20ns) and production run (10ns after Berendson).
Pressure 0.0300644 0.38 134.243 1.57106 (bar) Pressure -0.0405509 0.79 134.204 0.151638 (bar) Can someone please help me with this? Regards. Amin. ______________________________________________________________________ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202 -- 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
