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
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