<div dir="ltr"><span dir="ltr"></span><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank"></a><br><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;">
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Thanks to Jochen<br> </blockquote><div> To increase the lipid molecule number from 128(which downloaded from Dr.Tieleman site) to more than 158, I issued this command<br> genbox -cs 128popc.gro -o out.gro -box 9.2 9.2 6.3 but in the output file it showed unequal amount water molecules on both leaflets, I have tried in changing the box values in many ways but I couldnt able to get.<br>
Can any tell me how can I solve this problem to get increase in popc molecules with equal amount of water on both leaflets.<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><br>
I guess that depends on the size of your protein. You should have enough<br>
lipds such that the protein doesn't interact with its preriodic image.<br>
90 POPC seem to be a bit to few for that. In my aquaporin simulations, I<br>
usually had something like 270 POPE molecules, but if you simulate a<br>
smaller protein, less lipids may be sufficient. You may also want to use<br>
a hexagonal box which will allow you have less lipids and water.<br>
<br>
cheers, jochen<br>
<br>
sudheer babu wrote:<br>
> Hi gmx-users,<br>
> whats the number of POPC molecules should be there after inserting protein<br>
> into popc? In my case 90 popc molecules are there around the protein from<br>
> 128 molecues which I downloaded from Dr.Tielman's website.<br>
><br>
> Any suggestion will be appreciated<br>
> Thanks in advance.<br>
><br>
><br>
><br>
> ------------------------------------------------------------------------<br>
><br>
><br>
Dr. Jochen Hub<br>
Max Planck Institute for Biophysical Chemistry<br>
Computational biomolecular dynamics group<br>
Am Fassberg 11<br>
D-37077 Goettingen, Germany<br>
Email: jhub[at]<a href="http://gwdg.de" target="_blank">gwdg.de</a><br>
Tel.: +49 (0)551 201-2312<br>
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End of gmx-users Digest, Vol 53, Issue 81<br>
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