[gmx-users] Re:Unequal water of Bilayer system in *PR step

[Justin A. Lemkul]

sudheer babu wrote:
> -
> 
> 
>      
>      > Hi Users,
>      >     I have extended the lipid bilayer(popc) from default
>     popc128a.pdb to
>      > 200 popc molecules with suffcient water by using genbox.
>      > genbox -cs  128a.pdb -o  out.gro  -p  128a.top -box 9.2 9.2 6.9,
>      to the
>      > out.gro(contain 200 popc) minimisation ran fine later swtich over
>     to *PR
>      > with fc-1000 on P8,C51,C53 of popc and saw output_pr.gro in VMD
>      water has
>      > weird strcuture(up side downs but popc structure is quite fine).
>      > So I have reduced the pbc box size to 9 9 6.7  with *editconf
>     later I ran
>      > minimsation and *PR, "now water" and POPC structures are "fine" but I
>      > observed "unequal water".
> 
>  
> 
>     What do you mean with "unequal water"?
> 
>         Thanks for the response unequal water means ' when I noticed the 
> intial 200popc.gro use VMD water molecules present bothsides almost same 
> towards corners of the simulation box and centre of the above and below 
> popc heads but after *PR one side of the leaflet bilayer corners have 
> very less water (say 20 water molecules earlier 80 water molecules) 
> looks at corners doesnt have water seems. I hope you understood my problem,
> 

Probably your system isn't perfectly centered within the box and you are seeing 
"diffusion" from PBC.

-Justin

> Could you tell me any suggestion
> Thanks in advance.
> 
> 
>      >
>      > Could you tell me, did I miss something to use
>      > Any suggestions would be appreciated
>      > Thanks in advance
> 
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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