<div dir="ltr"><span dir="ltr">-</span><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
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> Hi Users,<br>
> I have extended the lipid bilayer(popc) from default popc128a.pdb to<br>
> 200 popc molecules with suffcient water by using genbox.<br>
> genbox -cs 128a.pdb -o out.gro -p 128a.top -box 9.2 9.2 6.9, to the<br>
> out.gro(contain 200 popc) minimisation ran fine later swtich over to *PR<br>
> with fc-1000 on P8,C51,C53 of popc and saw output_pr.gro in VMD water has<br>
> weird strcuture(up side downs but popc structure is quite fine).<br>
> So I have reduced the pbc box size to 9 9 6.7 with *editconf later I ran<br>
> minimsation and *PR, "now water" and POPC structures are "fine" but I<br>
> observed "unequal water".<br>
</blockquote><div> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">What do you mean with "unequal water"?</blockquote><div>
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,<br>
<br>Could you tell me any suggestion<br>Thanks in advance.<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
><br>
> Could you tell me, did I miss something to use<br>
> Any suggestions would be appreciated<br>
> Thanks in advance<br>
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