VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 05 2015 - 20:13:06 CST

JC,
  Unless there's a bug I'm not aware of, this should not prevent
you from writing to the velocity arrays at any time. I use this
scheme for all optional data arrays to save memory. If you query
an array that doesn't exist, you get zeroes, but on first write,
the memory should be allocated and stored to. Let me know if you're
having trouble with anything specifically?

Cheers,
 John

On Thu, Nov 05, 2015 at 08:56:46PM -0500, JC Gumbart wrote:
> Hi John et al.,
>
> We have a problem where we would like to store velocity data for a molecule. However, it seems this array only gets initialized if the filetype already contains such data. This is what I see in MolFilePlugin.C
>
> > // allocate space for velocities only if
> > // 1) the plugin implements read_timestep_metadata;
> > // 2) metadata->has_velocities is TRUE.
> > float *velocities = NULL;
>
> Is there any way around that? We???d rather not have to use TCL lists to store the data (too slow).
>
> Thanks!
> JC 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
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