Can you simulate the membrane and protein seperately, thus the two system you are trying to merge?
Gerrit > > 4. 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://lists.gromacs.org/pipermail/gmx-users/attachments/20110107/b897663b/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Fri, 07 Jan 2011 10:07:27 -0500 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Requesting advice on pressure scaling in a > protein-in-membrane system. > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4d272c2f.2070...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > 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 > > ======================================== > -- 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
