RE: Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints )

From: JC Gumbart (
Date: Wed Jun 29 2005 - 09:40:41 CDT

Water molecules should not penetrate past the lipid head groups regardless
of restraints. Perhaps the lipids need to be equilibrated more? You could
do this for a few hundred picoseconds while strongly restraining the water

SMD tracks the center of mass of all included atoms. It then applies forces
appropriately on all the atoms. If you use it with a velocity of 0, it
should do what you want to do.

-----Original Message-----
From: [] On Behalf
Of Sascha Tayefeh
Sent: Wednesday, June 29, 2005 9:31 AM
Subject: namd-l: Adding Misc. Potentials (e.g. spherical/repulsive
restraints/constraints )

 Hi all,

 there have been quite a few postings to this topic here (see
"constraining center of mass...", Feb 17 2005, or "can i restrain the
center of molecule...", Apr 20 2004), which have remained unanswered.
Facing similar problems, I'd like to give it another try:

 I've desperatly been trying to find a way adding planar restraints to a
membrane/protein simulation in order to avoid water molecules
penentating the membrane. In order to do so e.g. in Charmm, one would
use its so-called MMFP (Misc. Mean Field Potential) commands. What would
be the workaround in NAMD?

 Further, I would like to prevent drift of the membrane during
production run by referring to the center of mass of the complete
membrane rather than restraining each of the membrane's atom. How to do

 Last, I need to define a cylindrical potential function to prevent
drift of the protein. Any idea?

 Thank you for any suggestions!

Sascha T.

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