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

From: JC Gumbart (
Date: Wed Jun 29 2005 - 11:18:23 CDT

I'm not sure if it is available on the website but here is a script to keep
water molecules out of the membrane. The comments in the script tell you
how to call it from your configuration file.

Obviously, some adaptation of the script may be needed so look over it

-----Original Message-----
From: [] On Behalf
Of Sascha Tayefeh
Sent: Wednesday, June 29, 2005 9:57 AM
To: JC Gumbart
Subject: Re: namd-l: Adding Misc. Potentials (e.g. spherical/repulsive
restraints/constraints )

 Dear Mr Gumbart,

 thank you for your quick reply. I should have mentioned, that I am
trying to build the membrane "from scratch" with respect to a protocol
by Roux et al. The strategy consists of assembling a representative
starting configuration, using randomly selected lipids from a
preequilibrated set. The single lipids are disposed around the protein.
The *bilayer*, however, is far from equilibrium and approx. 1ns of
equilibration is nessessary. During this phase, water must be prevented
from penetrating the lipid head groups.

 As far as the center of mass problem is concerned, thank you very much
for the SMD hint, I will give it a try.



JC Gumbart wrote:

>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
>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!
> Sincerly
>Sascha T.

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