[gmx-users] About the Diffusion of Water Molecules
scvsankar_agr at yahoo.com
Tue Feb 5 16:44:40 CET 2013
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 ?
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