[gmx-users] About The Diffusion of Water molecules in Protein Lipid Simulation

Justin Lemkul 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.
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