[gmx-users] problem with undistribution of water

Maik Goette mgoette at mpi-bpc.mpg.de
Fri Mar 7 09:22:16 CET 2008

That "problem" is called periodic boundaries.
Try inserting a second bilayer to get, at least on one axis, a water 
layer between the two lipid layers, if you want to prevent PBC for a 
part of the waters.

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

sudheer babu wrote:
> Thanks Mr .Justin for your response,
> I am describing answers for  your questions,
> 1.My box size is 6.0nm in xyz dimensions.
> 2.The forcefield  I am using "ffgmx.itp" for membrane which I downloaded 
> from Pieter Tieleman webiste and deprecated FF for protein.
> 3 .I inserted protein into membrane by using genbox command.
> 4. I used force constant 10000 on protein.
>   There is no leaking of membrane, the stucture is fine till EM, but in 
> PR the water molecules are moving from one side of the bilyaer to the 
> other side. No water mol between lipid bilyer hydrophobic region. Ok I 
> tell you in clear way, Assume on membrane  each side 200 water molecules 
> are there but after equilabration 30 to 50 water molecules are reaching 
> other side , so one side its appearing  more  rather than other side.  
> But it looks in cubic form how appears in EM but only increasing water 
> molecules on other side. Popc and protein are fine. Will it cause any 
> problem later when I run further simulation by taking this output file.I 
> hope you got my problem.
> Thanks in advance.
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list