[gmx-users] Re: groups to write to trr

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Aug 24 17:32:49 CEST 2008


In this specific case it could be worth replacing writing .xtc files
(using xtc-grps, nstctxout, etc) with writing .trr files in the code.
That wouldn't be a lot of work (if you know a bit of C-code ;)).



On Sun, Aug 24, 2008 at 5:26 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Vitaly Chaban wrote:
>>> The risk you take with specifying trr-grps in an .mdp file
>> In the .mdp you can specify  to write no TRR coordinates at all and it
>> will be the same. :)
> Quite true, the only concern I have about implementing this new option would
> be novice users who blindly use it, thinking that it would be of benefit to
> save disk space.  As soon as something goes wrong, and they can't restart
> their run, we'll see dozens of emails about it :)
> This is not a problem for you, because you know what you're doing.  I
> suppose the trr-grps option would be fine, provided there are noticeable
> warnings in the documentation about using it.
> My C skills are weak, but how difficult would it be to implement this change
> within your current version, basically mirroring the code for xtc-grps?
>  Again, I don't know if that would be substantially difficult or not, but
> you might be able to do it and have the option immediately available to you
> :)
> -Justin
>> Really huge files are obtained if to write everything to .trr. It's
>> almost impossible to have several runs at once because of disk space
>> overflow. Now, we are limited not by processor time but by disk space.
> --
> ========================================
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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