[gmx-users] g_gyrate

[Anton Feenstra]

Dallas Warren wrote:
> 
>> You can still first do it 'manually' with trjconv, with the added 
>> advantage
>> that it only has to be done once, and you can check if it is done the way
>> you expect it to. Having said that, the last time I tried either -pbc 
>> nojump,
>> or the 'cluster' option, it didn't work the way I expected (but I also 
>> did
>> not have time then to get to the bottom of it).
> 
> 
> Yeah, I have some trajectories where it does an OK job, others where I 
> have tried so many options and combinations to try and get it to get 
> things all together in the center of the box, to no avail.
> 
> What I was actually suggesting is that the scripts can go over the pbc, 
> out one side and in the other, as if it was within the box.  Since it is 
> continuous anyway with the simulation, shouldn't it also be with the 
> analysis scripts?

Yes, the code at least is all there. But there are special issues to consider.
For calculating distances, having all *atoms* in the box is easiest. For fitting
and RMSD calculation, however, you'd like whole *molecules*, unless you want
to fit aggregates or other types of grouped molecules (co-factors, ligands),
then you need some way to tell the analysis tool which things belong together.

I think, if we'd use PBC aware routines throughout, all should work itself out
automatically. But, that would need a major overhaul of all tools. Having done
several minor overhauls myself, I know this is no small task...


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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