From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Thu Oct 22 2009 - 12:14:46 CDT
Hey Lucie,
Try "coorfile skip":
http://www.ks.uiuc.edu/Research/namd/2.7b1/ug/node10.html#SECTION00052200000000000000
Cheers,
Jerome
2009/10/22 lucie delemotte <lucie.delemotte_at_gmail.com>:
> 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
>
> Lucie
>
>
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