[gmx-users] unable to equilibrate pressure in npt

amin at imtech.res.in amin at imtech.res.in
Thu Jul 25 18:22:35 CEST 2013

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

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?


सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
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