From: Axel Kohlmeyer (
Date: Fri Nov 21 2008 - 03:45:39 CST

On Fri, 21 Nov 2008, dipti lele wrote:

DL> Hello all,

hello deepti,

DL> I am very new to NAMD. I want to analyse the results which i have
DL> obtained after MD run in NAMD. Now I want to analyse Maxwell- Boltzmann
DL> energy distribution. But I am not able to load .vel file in VMD. I have
DL> tried using file type as NAMD binary coordinates but it says that there are
DL> incosistent atoms in .vel file. I have also checked with the number of atoms
DL> and they are same in .psf as well as .vel file. I dont know why I am getting

you are getting this error, because VMD does not (yet) support
reading velocities. this is in the works, though.

DL> this error. How should I proceed now? Is there something wrong in the MD
DL> run due to which this error might occur?

the more interesting question is, how would you have proceeded
in case VMD could have been able to read the velocities?
in principle one can hack the molfile plugin readers to read
velocities as coordinates.


DL> Thanking you ..
DL> With Regards,

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.