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

vidhya sankar scvsankar_agr at yahoo.com
Wed Nov 28 10:24:55 CET 2012

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

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

Also How to include this Restraint in .mdp just Like using -D Flag ? 

Thanks In Advance

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