[gmx-users] Membrane Simulation

[Justin Lemkul]

On 4/18/13 10:59 AM, Giuseppe wrote:
>
>
> Dear all
>
> I'm trying to start a simulation with a protein embedded in a bilayer of
> POPC molecules, but I have some problems when I pack the lipids around the
> protein. Infact I place the protein in the proper position using the
> editconf tool with the “-rotate” and “-center” options on, but when I scale
> the lipid positions with the perl script (before the energy minimization),
> the protein moves up, de facto off from the membrane! Obviously I've set
> very strong position-restraining force on protein, but it moves the same.
> Probably the problem is trivial, but I can't see it, so any help is much
> appreciated.
>

You probably haven't set up the protein's location in a box with the same 
dimensions as the membrane, so it's centered within some different unit cell.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================