[gmx-users] About the Diffusion of Water Molecules

[Justin Lemkul]

On 2/5/13 10:44 AM, vidhya sankar wrote:
> Dear Justin Thank you for your Previous reply,
>
>
>                                                                              I am following your Protein -Lipid tutorial . I am doing simulation of Assembly of  Cyclic Peptide
>
> ( Made up of Only Phenyl alanine Residue) in DPPC lipid . After I have Attained suitable  APL  (69 A^2)   I solvated,  neutralized  (using genion)  & EMzed . Finally I Have Done NVT equilibration  Using Restraint on all atoms of  Lipid Molecules  . At the End of My simulation I Have observed   some of water molecules (60 water Molecules )   in Hydrophobic Part of Lipid Molecules (Amidst of Assembly of cyclic peptide)
>
> How to Avoid this ?
>
> Should Further Shrink APL using Perl And Then Proceeding NVT Equilibration ?
>

It doesn't make any sense to me to restrain all atoms of the lipids.  I would, 
at minimum, run NVT with no restraints on the lipids, and perhaps add a vertical 
restraint on water O atoms to prevent them from leaking into the membrane during 
the initial equilibration.  Then equilibrate again for a longer time with no 
restraints on either water or lipids.

-Justin

-- 
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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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