[gmx-users] Snapshots in different files

Arik Cohen acohen at biochem.duke.edu
Thu Oct 8 00:26:54 CEST 2009

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.
> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before 
> posting!
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> ------------------------------------------------------------------------
> No virus found in this incoming message.
> Checked by AVG - www.avg.com 
> Version: 8.5.421 / Virus Database: 270.14.5/2419 - Release Date: 10/07/09 05:18:00
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091007/78ad8a69/attachment.html>

More information about the gromacs.org_gmx-users mailing list