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

sudheer babu sudheer.pbm07 at gmail.com
Fri Sep 26 12:51:48 CEST 2008

> > 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,

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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