[gmx-users] Unequal water of Bilayer system in *PR step
sudheer.pbm07 at gmail.com
Fri Sep 26 09:48:24 CEST 2008
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
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