[gmx-users] POPC simulation

[Mark Abraham]

chris.neale at utoronto.ca wrote:
>> 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