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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--
========================================
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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