[gmx-users] About The Diffusion of Water molecules in Protein Lipid Simulation
scvsankar_agr at yahoo.com
Mon Nov 5 14:20:37 CET 2012
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)
Thanks In Advance
More information about the gromacs.org_gmx-users