[gmx-users] Re: Simplified molecular dynamics

David spoel at xray.bmc.uu.se
Sat Nov 13 10:06:06 CET 2004

On Fri, 2004-11-12 at 13:53 +0100, Sandor Pongor wrote:
> Dear David,
> I am interested in doing a very simplified, symbolic molecular dynamics
> run for 5-10 "atoms" interconnected with a simple "bonds" that can be
> broken. I figured that the best way would be to use a ready program, and
> tinker the force field so that there are only two elements left:
> specific interaction (strong Lennart Jones)
> aspecific interaction (aggregation, weak Lennart Jones).
> As I looked around on the net, I found your note "Lennart Jones only" to
> gmx users. Is gmx a latter day version of GROMOS? Is this modelling
> possible with the program? What I would like to do is to follow the
> dynamics and plot various quantities along the trajectory. I think it may
> be possible by using single atoms (like metal atoms), by defining the
> e(ij) quantities in a suitable manner, and then deleting or switching off
> all other interactions (like electrostatics). 
> It has been a very long time since I saw a MD program with my own eyes, so
> this may be a bit naive. Nevertheless, I would appreciate your notes. Also
> if you can suggest other programs that can be used, in my neighborhood
> peopla are running Sybil etc.
It would be quite straightforward to do what you want, if you think you
can model it with Lennard Jones only. By it's very nature the LJ
interaction is very weak at long distances. Alternatively you can define
morse bonds between the atoms, but then no new bonds can form during the
simulation since it is a fixed list. For a small number of atoms you
could, however make a full matrix of bonds between all atoms, although
I'm not sure whether that would be a stable numerically, probably
depends on the potential well depth.

GROMACS uses the (among other) GROM0S force fields, and it was initially
(15 years ago) written as a GROMOS clone. Since then GROMACS has evolved
a lot and GROMOS has been rewritten from scratch as well.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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