[gmx-users] POPC simulation
chris.neale at utoronto.ca
Fri Nov 2 00:43:27 CET 2007
>> >> 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.
>Someone who actually does this sort of simulation should check it over
>and expand as appropriate. Chris? Tsjerk?
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.
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