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

Xavier Periole X.Periole at rug.nl
Fri Sep 26 11:49:54 CEST 2008

On Fri, 26 Sep 2008 13:18:24 +0530
  "sudheer babu" <sudheer.pbm07 at gmail.com> 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"?
> Could you tell me, did I miss something to use
> Any suggestions would be appreciated
> Thanks in advance

XAvier Periole - PhD

Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands

More information about the gromacs.org_gmx-users mailing list