[gmx-users] Coordinate file for lipid bilayer

[Justin A. Lemkul]

On 6/11/12 6:05 AM, James Starlight wrote:
> Dear all!
>
>
> Recently I've forced with the opposite problem. I have pre-equilbrated bilayer
> of highter dimensions than I need. How I could reduce lipid number of such
> bilayer as well as reduce total dimensions of such system ?
>
> E.g I have preequilibrated bilayer consisted of 340 lipids. I want to reduce it
> to the 200 lipids by the symmetrical deletion of the unnecessary lipids from
> each side. Is there simplest way to do it ?
>

Try genbox with the -box option (with your bilayer as -cs) to set a smaller box 
size that will give a suitable number of lipids.

-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

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