[gmx-users] Requesting advice on pressure scaling in a protein-in-membrane system.

Daniel Adriano Silva M dadriano at gmail.com
Fri Jan 7 16:03:15 CET 2011

Dear gmx users and developers,

I am facing a problem that is new for me and I will appreciate advice from
your expertise. I am working with a big protein complex (around 100K atoms,
several subunits) and I used g_membed to embed it in a (aprox 24 14 nm)
pre-equilibrated POPC membrane, however after embedding and a 1ns of NVT
equilibration I tried to proced to the NPT equilibration, but I found my
system exploding (things moving to fast), so I tried several methods that
came to my mind (like decrease the P-coupling constant, decrease the
timestep and some others). After few tries I went back to the
NVT  equilibration and took a look to the pressure, for my surprise I found
it to be around 1e30! So I ended with a very compressed system on X-Y, I
guess given the embedding of the protein in the membrane. Here are the

1) Are there any reasonable simple method to reduce the pressure on the
protein/lipid system?
2) May I expect a very long time to reach the adequate pressure and
equilibrium given a possible change on the phase of the lipids by the high
3) Any other useful direction?

Extra information: On this step I had frozen the Protein and excluded the
Protein-Protein energy.

Daniel Silva
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