[gmx-users] Simulation of membrane protein
jmsstarlight at gmail.com
Sat Oct 29 11:30:14 CEST 2011
It's appeared new question about G_membed
Does anobody used this algorithm for insertion of their proteins ?
In particular I wounder to know how I can to find optimal parameters (
different scaling factors like in the below command) for insertion in my
system( single alpha helix in DMPC bilayer system) and how I can measure
area per lipid in the output system?
g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000
-zinit 1.1 -zend 1.0 -nz 100
2011/10/25 Justin A. Lemkul <jalemkul at vt.edu>
> James Starlight wrote:
>> I've found the same task of MSU's students :) They simulate membrane
>> formation without NPT stage ( after NVT they run production MD). From they
>> reports I've found that simplest membrane system could be formed within
>> 10-30 Ns. But what about try to make such simulation in vacuum at first
>> without any water ? Might the bilayer been formed in such conditions?
>> Finally I have small question about pereodic boundaries of such bilayer
>> E.g I've done simplest system with water consisted of 8 lipid molecules +
>> some water.
>> This is the representation of the system http://i1209.photobucket.com/**
>> I want to simulate bilayer formation as well as concomitant hydrophobic
>> effect ( removing all water from formed bilayer)
>> Does the PBC presented in that example ( 2.64196 2.64196 6.85002 for 8
>> lipids) are enought for such lipid movement? It seems that more free space
>> aree needed for overal turn of lipid molecules. How I can calculate exactly
>> PBC value required for my system ?
> I agree that your system has insufficient space for any real movement
> without violating the minimum image convention. Your system must have
> adequate room for any lipid to rotate in any direction, and be of sufficient
> size to accommodate a formed membrane, which will have dimensions dictated
> by the APL for the chosen lipid (and of course, the force field's ability to
> produce that value).
> 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users