[gmx-users] About the Diffusion of Water Molecules

Justin Lemkul 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list