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

sudheer babu sudheer.pbm07 at gmail.com
Fri Sep 26 09:48:24 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".

Could you tell me, did I miss something to use
Any suggestions would be appreciated
Thanks in advance
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080926/89243f93/attachment.html>

More information about the gromacs.org_gmx-users mailing list