[gmx-users] POPC simulation

[Chris Neale]

>
>> >> 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.