[gmx-users] About Diffusion of water Towards Tail part of Lipids

[Justin Lemkul]

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
> #endif
>

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

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

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

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