Re: extracting time from DCDs

From: Brian Bennion (
Date: Fri Jan 14 2005 - 14:10:02 CST

Hello Erik,

Below is a snippet of a BIOCORE conversation Jim and I had
regarding timesteps embedded in DCD files.

Hope it is helpful.

(9/29) 11:57 jim NAMD 2.5 has just been released.
(10/16) 10:05 bennion1 Jim, I was writting some code to read
through dcd files and am curious about the format of the timestep entry.
(10/16) 10:06 bennion1 In dcdwrite in namd it is a float(real*4
in fortran) but I can't read anything sensible using real *4 variables...
(10/16) 10:06 bennion1 instead of being 1.0 or 2.0 it is 0.049
(10/16) 10:07 jim The units are hideous.
(10/16) 10:07 bennion1 is there a problem when casting the double
to float in the dcdwriting routine?
(10/16) 10:09 bennion1 I am a little confused by your last
(10/16) 10:10 bennion1 I think you have done a great job
emulating a formatted fortran file
(10/16) 10:14 jim Multiply by 48.88821 to get fs, check your email
for the explanation.
(10/16) 10:22 bennion1 Know I know why you said they were
hideous...thanks for the help

On Thu, 13 Jan 2005 wrote:

> Hi folks... it seems like this should be an easy question, but I haven't
> been able to find an answer for it myself. What I want to do is extract
> the value of the simulation time (or, just as good, the timestep number)
> from particular frames in a DCD trajectory. I'm using VMD for my analysis,
> but I haven't seen anything in the docs that refers to doing this.
> Obviously, this information could be recontructed from a knowledge of
> the NAMD timestep, firsttimestep, and DCDfreq parameters (which I do have),
> but I'd much prefer a foolproof way of getting this info directly.
> Is the timestep in fact part of the DCD data structure?
> I'm probably just missing something simple... but can anyone point the way?
> thanks!
> - Erik
> C. Erik Nordgren, Ph.D.
> Department of Chemistry
> University of Pennsylvania

**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:29 CST