[gmx-users] Re: Prosessing of the pre-eqilibrated lipid bilayer

James Starlight jmsstarlight at gmail.com
Mon Oct 31 14:29:26 CET 2011

So does anobody know possible sollution for the reduce size of the existing
E.g I've preequilibrated 128 lipids in bilayer and want to obtain 32 lipid
bilayer and dont perturb overall topology of the system
In my lab there is only extremely weak CPU. it could not make md for large
systems ;p

2011/10/30 James Starlight <jmsstarlight at gmail.com>

> Dear Gromacs Users!
> I wounder to know about possible algorithm of preparation of the existing
> lipid bilayer for further simulation.
> E.g I have some pre-equilibrated bilayer consisted of symmetrical lipid
> organization. Now I'd like to remove some lipids from the edges of my
> bilayer to reduce overall ammounts lipids but dont perturb symmetry of the
> system. Then I'd like to place this bilayer to the rombic box (
> corresponded to the organzation of the new bilayer system).
> How I could to realise such operation of the lipid removing ?
> In addition I'd like to check Area per lipid value during that removing.
> How this could be done?
> James
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