VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Mar 23 2010 - 12:00:04 CDT

On Tue, 2010-03-23 at 16:16 +0200, politr_at_huji.ac.il wrote:
> Dear all,
> I want to perform a molecular dynamics simulation with implicit solvent.
> Does anyone is familiar with such simulations and can suggest what
> should I use. Maybe I should use CHARMM

you can also try lammps. check out
http://lammps.sandia.gov/doc/pair_charmm.html

while lammps is a pretty bare bones MD code, you
can convert topologies generated with VMD/psfgen
to their native format and output dcd trajectory
files, so it is almost like using NAMD.

if you use only short range potentials, then LAMMPS
will parallelize quite well. at homogeneous, bulk,
plain LJ it is competitive to NAMD since there is
less load to balance and LAMMPS has a little less
overhead. for typical explicit solvent bio systems
with long-range coulomb NAMD is far better.

cheers,
    axel.

> Regina
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.