Re: NAMD feture request

From: Giacomo Fiorin (
Date: Wed Apr 13 2011 - 10:17:27 CDT

Hi Ajasja, you can compress the colvars.traj files quite a lot if you run
gzip or bzip2 on them. This way you can still analyze them with scripts (by
processing them on the fly with gzip -dc), rather than write specific
programs to even open them. To save extra space, have you considered doing
what you propose for the DCD trajectories, i.e. keeping only a subset of the
variables at high frequency, and instead the whole set at much lower

Saving the DCD files for a subset of the atoms can be useful in a few
specific cases, but on a general basis I would advise against it. Not
knowing at all what's happening to the lipid membrane and the solvent seems
a bit risky. At least the way you're doing now you can look at the whole
system and see that it looks OK before you can neglect the uninteresting


---- ----
  Giacomo Fiorin - Postdoctoral Researcher
  ICMS - Institute for Computational Molecular Science - Temple University
  1900 N 12 th Street, Philadelphia, PA 19122
---- ----

2011/4/13 Ajasja Ljubetič <>

> Dear NAMD developers,
> I have two feature request which are related, perhaps even mutually
> exclusive:
> - Would it be possible to add binary output for colvars trajectories?
> I would like to write several colvars at high frequency and the text
> files are getting into Gigabytes.
> - Would it be possible to implement writing only part of the system
> into the binary dcd trajectory.
> I have a medium membrane system, but I'm interested only in a small
> specific part. It would be ideal if NAMD could read a file of atom indices
> and write only those atoms to the dcd. (And I know I can run my simulation
> in parts and then load the trajectory in VMD and save only the interesting
> part and delete the oiginal dcd - this is what I'm doing now.)
> Best regards,
> Ajasja Ljubetič,
> Young reasercher,
> Laboratory of biophysics,
> Institute Jožef Štefan,
> Ljubljana, Slovenia

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