[gmx-users] Coordinate file for lipid bilayer

James Starlight jmsstarlight at gmail.com
Tue Oct 2 20:16:21 CEST 2012

Dear all!

Recently I've forced with the same problem as was in this topic :)

I have tieleman's lipids consisted of 128 dppc with water.
also I have system with the protein inserted in the same bilayer

I wounder to know

1- How I could change lipid number in the pure lipid bilayer (
increase up to 200 lipids) with standard Gromacs tools ?

I've tried use
genbox -cs dppc128_whole.gro -box 8.04542  8.04542  10.19156

where 8.045 in x and y was higher than in the case of initial bilayer ( 6.045)
As the consequence that prodyce larger system with increased amount of
water in upper and lower layers but the lipid number was the same.

2- Is there any way to increase lipid number ( to add lipids from each
size of the system) in the bilayer with the inserted protein ?

Thanks for help,


2012/6/11, Justin A. Lemkul <jalemkul at vt.edu>:
> 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
> ========================================
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