[gmx-users] About The Diffusion of Water molecules in Protein Lipid Simulation
jalemkul at vt.edu
Mon Nov 5 14:29:11 CET 2012
On 11/5/12 8:20 AM, vidhya sankar wrote:
> Dear Justin ,
> Thank you for your Previous reply
> I am following your Protein Lipid Tutorial
> After Several Shrinking and several EM of my system i reached the APL for DPPC 64am^2
> , I Have Added the ions to Neutralize the system . Then I have Done EM When I Visualize The system in VMD
> it was good As in the tutorial Web page
> Then I did NVT Equilibration , when i see the Resultant .gro file in VMD All the Lipid Molecules are just away from the protein ( which is Kept in center of Box)
> While some of the Water Molecules are nearer to Protein ( it means that during Equilibration water molecules are diffusing towards protein while Lipid Molecules are Diffusing Away from Protein Which is in the center) Is it correct or Wrong ?
> Where I have committed the Mistake ? Is my System Contains Voids ?
> Also Tail part of the Lipid molecules are protruding outside Box While Head part is in the Solvent Region (it means some Lipid Molecules Are flipped up)
I have no idea what has gone wrong. It sounds like whatever you've done to
build the system was incorrect.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users