[gmx-users] Removing water from sides of bilayer

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 6 13:22:27 CET 2009

krithika krishnaswamy wrote:
> hello,
> Am a new user to gromacs.how to add water to a bilayer.i tried adding 
> water to entire system and then removed water from sides using tcl 
> script.But its not working.
> Is there anyway to build lipid layer by layer and add water or something 
> can be done with genconf,genbox command so that water will not enter 
> middle region of bilayer.Please provide me with a detailed procedure.

There are several options listed on the wiki site:


I find the genbox method to work quite well, myself.  If you're getting water 
from the "sides" of your bilayer, then your box vectors are wrong (i.e., too 
large) for the system.


> -krithika
> ------------------------------------------------------------------------
> _______________________________________________
> 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


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list