[gmx-users] Visualizing MD trajectories

Erik Lindahl erik at theophys.kth.se
Fri Aug 24 10:08:47 CEST 2001

On Fri, 24 Aug 2001, Dr. Y. U. Sasidhar wrote:


> We have been using GROMACS 2.0  for nearly an year. We have used it on
> SGI, Compaq ( dec alpha ) with truunix64. While GUI iwas available on
> SGI, we could not use it on Compaq as MOTIF  was not installed. This was
> a drawback since we can not use ngmx for visualization. Further I prefer
> GUI to command line interface.

Well, first I'll warn you not to set your expectations too high - it's
not a complete GUI like a windows program, but rather a window where
you can select the command line options with buttons and menus.

> 1. Where can I get MOTIF for Compaq.

Motif should be included with all commercial unix variants, but you
might have to install some development package to get all the header

If you can't find this you can download the Lesstif clone from
http://www.lesstif.org for free (it's GPL). There are even binaries
for many platforms.

The Gromacs configure script will look for Motif automatically, but
if you have the libraries and header files in some special location
you might have use --with-motif-libraries= and --with-motif-headers=

> 2. What are other options to visualize MD trajectories generated by
> GROMACS. I am  aware of only VMD but have not used it much. What is your
> experience ?

VMD is nice, but somewhat big and bloated. gOpenMol (there's a link
on our homepage under other software) is a good alternative. It can't
draw the atoms in as many ways as VMD, but it can read all Gromacs
trajectories. You can even rotate the system while the trajectory
is playing! Both of these programs require OpenGL, though.

The ngmx viewer included in Gromacs is very slow compared to OpenGL
implementations, but the whole idea with it is that it will work even
across a slow X connection to a supercomputer without OpenGL...



Erik Lindahl, PhD                                erik at theophys.kth.se
Dept. Biophysical Chemistry, Groningen University, THE NETHERLANDS
Phone: +31 50 3634335    Fax: +31 50 3634800
(You can also reach me as lindahl at chem.rug.nl and lindahl at gromacs.org)
Hi! I'm a mutated .sig virus! Put me in ~/.signature to multiply me!

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