From: Julie Grouleff (
Date: Wed Mar 09 2011 - 04:56:53 CST

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?


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