From: Axel Kohlmeyer (
Date: Wed Mar 09 2011 - 06:04:00 CST


On Wed, Mar 9, 2011 at 5:56 AM, Julie Grouleff <> wrote:
> I have build a POPC membrane with the membrane builder plugin using the C36
> CHARMM parameters and then put a water box around it using the solvate
> plugin. My problem is that the topology of the waters from the membrane
> builder plugin and the solvate plugin is not the same, so now I have two
> "types" of waters in my system. The waters that come from the membrane
> builder plugin have an extra bond between the hydrogens and there is a
> remark in the topology file that this bond is needed for shake. I run my
> simulations in NAMD using the rigid water constraint ("rigidBonds water" in
> conf. file). Does this mean that I should have this extra bond for all the
> waters? Or should I remove this bond similarly to what has been done in
> prevoius vmd versions and simply add the constraint in the configuration
> file?

if you run your simulations in NAMD you don't have to worry.
the extra H-H bond is only needed in the charmm code for shake.
NAMD will ignore it with rigidBonds water.

if you want to remove the bonds for cosmetic reasons, i can
send you a little script that should fix that.


> /Julie
> --
> Ph.D. student
> Biomodelling Group
> Department of Chemistry
> Aarhus University
> Office 1510-421
> Tlf. +45 8942 3385

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.