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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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