[gmx-users] About Diffusion of water Towards Tail part of Lipids
jalemkul at vt.edu
Wed Nov 28 13:35:58 CET 2012
On 11/28/12 4:24 AM, vidhya sankar wrote:
> Dear Justin,
> Than you for your Previous reply
> Regarding Diffusion Of Water From Head of Lipids to Tail Part During NVT Equilibration, You Suggested My one question as follows
> May I freeze these molecules During NVT Equilibration) ?
> The better approach would be a position restrain along the z-axis only, allowing
> the lipids to perhaps re-orient and pack a bit better, followed by NVT
> equilibration in the absence of any restraints on water.
> My Question is If Need to use Restraint on Water . Should I Generate Separate water_posre.itp using genrestr tool ?
> Otherwise May I Edit ( it means Applying restraint only in fcz column and Making Zero for fcx and fcy columns )
> and use Default setting of restraint of water in .top files as follows
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
Modifying this section of the topology is the easiest thing to do. I see no
reason to run genrestr.
> Also How to include this Restraint in .mdp just Like using -D Flag ?
All #includes and defines work the same way.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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