Daniel Adriano Silva M wrote:
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.
During NVT? Turn off this freezing before proceeding, doing additional NVT if
necessary. Frozen groups can do weird things, and I would suspect that your
system simply isn't stable in the presence of these frozen groups.
I have a procedure (and troubleshooting tips) for equilibrating membrane protein
systems in my tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
You may find it useful. Membrane systems do take a while to converge, but
that's not your issue here. You have some fundamental instability to deal with
first.
-Justin
Thanks,
Daniel Silva
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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