[gmx-users] About the Diffusion of Water Molecules
jalemkul at vt.edu
Tue Feb 5 20:53:13 CET 2013
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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