From: Axel Kohlmeyer (
Date: Mon Feb 13 2012 - 16:57:22 CST

2012/2/13 Molybdos Kirkimpolakis <>:
> Dear VMD Masters,
> I was wondering how can I get the "Timestep" of each frame of my simulation
> after the files are loaded in vmd.

usually not. most trajectory formats don't store that information.
you can recover that information from your simulation timestep
and frequency of writing trajectory data.

> In addition I was also wondering how to use hbond command. When I type
> set protein [atomselect top protein]
> measure hbonds 3.5 30 protein
> I got a long list of numbers, Can anyone explain what it means or make an
> example of how to use it?

the explanation is in the VMD user's guide.

> I cannot use the pulgin, because I only have access to  a cluster where I
> can only run commands and no a graphical version of vmd.

the hbonds plugin can also be used in a text mode.


package require hbonds

and then you'll have a hbonds commands that does
everything the GUI does. in fact, the GUI simply collects
the command line flags. if you type "hbonds" without any
options, it will print a small help information.

which is also provided in the online documentation of the plugin.


> Thanks so much for your help!!
> --
> cheers
> Molybdos Kirkimpolakis
> Πανεπιστήμιο Πατρών

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.