[gmx-users] Snapshots in different files

[Arik Cohen]

Thanks for answering.
This would not be the case so much since another program(sniffer) can be 
working along side gromacs
examining each snapshot(Max 400 residues == atoms. I'm only interested 
in the C-alpha) and then  if all criteria are met to extract/or save the 
coor and if not to erase the snapshot.
The aim here is to do an MD from which an ensemble of the C-alpha will 
be created.

Thanks again

Arik

 
 
Mark Abraham wrote:
> Arik Cohen wrote:
>> Thanks allot, but isn't trjconv should be executed  after the 
>> trajectory has finished ?. I would like to put each snapshot in a 
>> different file on the fly.
>
> As Justin said, you can't do that. For starters, it consumes vast 
> amounts of disk. Also, it doesn't take long to do it after the fact on 
> some workstation, and it is wasteful to spend your (limited) main 
> compute resources doing I/O while post-processing output.
>
> GROMACS workflows are intended to run the simulation fast and 
> efficiently, and then allow you to process the results with the 
> various tools/filters to extract the data you need. You can even 
> post-process with mdrun -rerun if you want to get only a subset of 
> forces or something. The main exception to this principle is the use 
> of xtc-groups, IIRC.
>
> Why do you even want separate PDB frames? Visualization tools like VMD 
> will read the trajectory files.
>
> Mark
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