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

Mark Abraham Mark.Abraham at anu.edu.au
Sat Oct 20 02:53:53 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.

That would make the solution look elegant, but really just moves the 
crud from one place to another. Now all the trajectory analysis tools 
have to sanitize the users input more rigorously. I think making the 
user choose a simple-format trajectory file that already has (nearly) 
the subset of data they want is a better solution.

I do like the atom names and connectivity, though, which will make life 
nicer with some visualization software.


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