From: Axel Kohlmeyer (
Date: Wed Feb 23 2005 - 14:29:22 CST

>>> "JG" == Justin Gullingsrud <> writes:

JG> Hi,


just one remark: the gromacs plugin of the latest VMD (1.8.3)
should be able to write proper .trr trajectory files
(exactly to be able to use the gromacs tools for analysis).
you may prefer those over .pdb trajectories as they are binary
and thus are read _much_ faster.


JG> I've used the Gromacs programs g_covar and g_anaeig to perform
JG> analysis of NAMD-generated trajectory files by first converting the
JG> trajectory to sequential pdb format. You can do this in VMD by simply
JG> loading the dcd file and saving it as a pdb, but there is one caveat:
JG> you must change all the "END" lines to "ENDMDL", or g_covar will
JG> crash.

JG> Hope this helps,
JG> Justin

JG> On Tue, 22 Feb 2005 16:06:55 +0000, Philip Fowler <> wrote:
>> Hi everyone,
>> I really, really want to use the IED plugin for VMD
>> to analyse the principal components of my molecular dynamics simulations. But
>> I use NAMD (naturally) and I am having difficulty pre-processing the
>> trajectories using PTRAJ as recommended by the developers of IED. I have
>> tried both the freely available PTRAJ and the one that is part of the
>> AMBER8.0 package and each time it does not like reading my NAMD CHARMM .psf
>> topology file. (Error: "WARNING in scanDouble: ...scanning LES, lesfac")
>> Has anyone successfully managed to use IED to analyse NAMD trajectories (with
>> the CHARMM forcefield)?
>> Are VMD psfgen produced CHARMM .psf topology files incompatible with PTRAJ? I
>> haven't even been able to try out a NAMD .dcd file yet.
>> Any help would be greatly appreciated,
>> Thanks,
>> --Phil
>> --
>> Philip Fowler,
>> PhD Student
>> Centre for Computational Science,
>> UCL Chemistry

JG> --
JG> The spirit of Plato dies hard. We have been unable to escape the
JG> philosophical tradition that what we can see and measure in the world
JG> is merely the superficial and imperfect representation of an
JG> underlying reality.
JG> -- S.J. Gould, "The Mismeasure of Man"

Axel Kohlmeyer       e-mail:
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum
If you make something idiot-proof, the universe creates a better idiot.