Pair interaction runtime analysis skipping dcd frames

From: lucie delemotte (
Date: Thu Oct 22 2009 - 09:30:08 CDT

Hi Namd users,

I'm trying to run an analysis using the following script at the end of
the configuration file on a dcd that was saved every 1000 timsteps.

set ts 0
firstTimestep $ts

coorfile open dcd mydcd.dcd

while { [coorfile read] != -1 } {
  incr ts 1000
  firstTimestep $ts
  run 0

coorfile close

I'd like to skip some data and do the analysis every 10,000 steps only
(so skip 10 frames in my dcd).
However, when I increase ts by 10,000 (incr ts 10000) it doesn't work
as I expected since it does the pair interaction calculation every
time step but replaces the time step by ten times its value.
In the end, instead of having an analysis with 1,000,000 steps, it has
10,000,000 steps.

Is there any way of doing this ? (Other that using catdcd which is not
that convenient for my purpose!)

Thanks for the help


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