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

vidhya sankar 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

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