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

Justin A. Lemkul jalemkul at vt.edu
Sun Aug 24 17:26:54 CEST 2008

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 :)


> 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


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