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

[Tsjerk Wassenaar]

Hi,

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 ;)).

Cheers,

Tsjerk

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
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
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