>> Hi
>> I want to perform peptide + popc membrane simulation. I download >> popc128a.pdb from >> >> (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies). >> Before I introduce the peptide into the membrane, the water layer >> had to be broadened to ensure full solvation of the peptide .I >> increase the water layer using the following commands >> 1. editconf -f popc128a.pdb -o po_box.pdb -box 6.1065 >> 6.1059 9.0000 -c
>>   2. genbox  -cp  po_box.pdb  -cs  -o  po_sol.pdb  -p  lip.top
>>
>> Now, the no. of water molecules over the bilayer increased . But, >> the problem is that there are water molecules inside the bilayer, >> which were absent incase of popc128a.pdb. How can I remove these >> offending water molecules?
>>
> > Did you search? > > Search "water membrane" = first hit:
> http://www.gromacs.org/pipermail/gmx-users/2007-March/026289.html
> > I and others also answered this question one week ago. Here is some info > from that:
> http://www.gromacs.org/pipermail/gmx-users/2007-October/030361.html
> http://www.gromacs.org/pipermail/gmx-users/2007-October/030400.html
> > This probable deserves a wiki entry.

Done... http://wiki.gromacs.org/index.php/Membrane_Simulations
Someone who actually does this sort of simulation should check it over and expand as appropriate. Chris? Tsjerk?

Mark

Looks great. Thanks Mark. The combination of a wiki with a mailing list is certainly benificial. I'll add to it as I have the time and as questions come up on the list.
Chris.


_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to