[gmx-users] Re:Unequal water of Bilayer system in *PR step
Justin A. Lemkul
jalemkul at vt.edu
Fri Sep 26 13:30:13 CEST 2008
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.
> 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
jalemkul[at]vt.edu | (540) 231-9080
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