[gmx-users] Snapshot taken under certain condition

Arik Cohen acohen at biochem.duke.edu
Wed Oct 7 03:25:57 CEST 2009

Thanks allot for all your help


Mark Abraham wrote:
> Arik Cohen wrote:
>> Dear users,
>> Is there a way(in the mdp file) to take a snapshot of only the 
>> C-alpha atoms along a trajectory if certain condition are met(tested 
>> every time a snapshot needs to be taken) ?
> If you know in advance you'll only ever want the C-alpha atoms for 
> analysis (dangerous) then you can use xtc-groups to write only that 
> set. Better is to savee all the data you might want, and then filter 
> for the C-alpha atoms with trjconv at a suitable point.
> You cannot apply your condition during the simulation, but must apply 
> it after the fact. For example, use a suitable analysis tool, and then 
> perhaps post-process that output to provide input to trjconv to 
> extract the frames of interest. The detail of the necessary procedure 
> will depend on the nature of the condition you want to apply.
> 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: 8.5.420 / Virus Database: 270.14.5/2418 - Release Date: 10/06/09 18:34:00
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091006/cb6adc3e/attachment.html>

More information about the gromacs.org_gmx-users mailing list