[gmx-developers] multiple xtc output files (optionally in chunks)

David van der Spoel spoel at xray.bmc.uu.se
Fri Oct 19 22:37:26 CEST 2007

Erik Lindahl wrote:
> Hi,
> On Oct 19, 2007, at 5:33 PM, Bert de Groot wrote:
>> Berk Hess wrote:
>>> How many different time scales could one have?
>>> A solution which I actually did use (so now I do remember having needed
>>> something
>>> like this) is applying trjconv after each 24 hour queue run to select
>>> the parts
>>> of the xtc files I wanted at different frequencies.
>>> So would 2 be enough?
>> I'd estimate that two is enough for most practical purposes. But if 
>> it's not
>> much more complicated to implement it in a fully flexible way, then 
>> I'd prefer that.
> I guess another alternative is to introduce a group concept in a more 
> general trajectory format (we've been thinking of having formats that 
> include at least atom names and connectivity in a header) so that a 
> single file can have different contents in different frames.

there is also a feature request for forces for subgroups, so why not 

problem when you start generalizing this kind of thing is that it turns 
from a quick hack into a big project.

We already have xtc_groups, but in this case only the first group is 
written. This could be changed into writing ctraj_group1.xtc, 
ctraj_group2.xtc and so on. Same with normal trajectories.

One has to be careful with file formats like xtc and trr, in that they 
in principle support to have different number of coordinates each time, 
but that may (will!) in fact crash analysis tools. Maybe we should 
disallow this feature, if only because you probably won't know what you 
get in these cases.

The best option would be to have file formats that always have the same 
number of atoms in each frame. In addition it would be worthwhile to 
store the atom names such that analysis tools don't need tpr files anymore.

> Cheers,
> Erik_______________________________________________
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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