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

[Daniel Adriano Silva M]

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
questions:

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
pressure?
3) Any other useful direction?

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

Thanks,
Daniel Silva
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110107/b897663b/attachment.html>