[gmx-users] Snapshots in different files

Dallas B. Warren Dallas.Warren at pharm.monash.edu.au
Thu Oct 8 01:51:18 CEST 2009

If the time frame between snapshots is not too short, you could have
that as the length of each MD run, then simple extend the run to keep on
going.  Could be a bit inefficient.  (This is how you should run MD
anyway, to ensure don't lose a lot of information if the computer system
you are running on crashes etc.)


I wouldn't be too surprised if it was possible to hack the code so that
a coordinate file is spat out at some interval (even with a limited
index of atoms).  But that is something for those that know the ins and
outs of the code to tell you.


Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology 
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
When the only tool you own is a hammer, every problem begins to resemble
a nail. 


From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Arik Cohen
Sent: Thursday, 8 October 2009 9:27 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Snapshots in different files


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 


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. 

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