VMD-L Mailing List

From: Eugene Leitl (eugene.leitl_at_lrz.uni-muenchen.de)
Date: Sat Mar 25 2000 - 19:03:56 CST

Kemikal Kid Kolby writes:
> Hi this is Kolby from the photosynthesis center at ASU. I was wondering
> if anyone knew how to model bilayer membranes or liposomes with VMD.

VMD is just visualization. You need to have another package to run it
on.

I was able to model ~50 kAtoms lipid bilayer systems with EGO (64
MBytes K6/200 Linux box), and was able to visualize them with VMD. You
can see some of my (amateurish) work here:
http://homes.acmecity.com/thematrix/gift/202/research/s0.html

Of course, the proper program to use with VMD is NAMD. I haven't tried
it in on a PVM box yet, however.

Have also a look at Helmut Heller's site.

http://www.lrz-muenchen.de/~heller/membrane/membrane.html
http://www.lrz-muenchen.de/~heller/ego/index.html

Try also
http://www.mpibpc.gwdg.de/abteilungen/071/solvate/docu.html
http://www.mpibpc.gwdg.de/abteilungen/071/

If you're talking liposomes, you're obviously talking serious system
sizes. The water alone will kill you, unless you can restrict
hydratation to a shallow layer both inside and outside of the lipid
bilayer.

I would be interested if you could keep us posted on your progress.

> Thanks!
>
> -Kolby