[gmx-users] demixing REMD trajectories

[David van der Spoel]

madeleine.kittner at mpikg.mpg.de wrote:
> Hi gromacs users,
> 
> I ran a REMD simulation of 2 peptides in water using 50 replicas. To check
> the consistency of the REMD system I want to check the structure
> distributions of each replica. For that I need to demultiplex the
> (temperature) trajectories. I attempt exchanges every 5ps and save data
> every 20 ps.
> 
> I used the demux.pl script to generate replica_index.xvg and
> replica_temp.xvg which look fine. But if I try to generate continuous
> trajectories for each replica using
> 
> trjcat -f traj*.xtc -demux replica_index.xvg
> 
> I get...
> 
> Read 50 sets of 17272 points, dt = 5
> 
> Reading frame       0 time    0.000   Segmentation fault
> 
> Is the problem caused by the fact that the number of time frames in the
> trajectories don't match the number of time frames in the replica index
> file?
> I read through the earlier postings on this subject, after using demux.pl
> everyone seemed satisfied. So, I guess it works somehow and I just do
> something wrong I can't figure out.
do you have the same number of xtc files as there are columns in the xvg 
file?

> 
> Thanks for your help.
> Cheers,
> Madeleine
> 
> 
> ---
> 
> Madeleine Kittner, PhD student
> Department of Theory and Bio-Systems
> Max Planck Institute of Colloids and Interfaces
> Research Campus Golm
> 14424 Potsdam, Germany
> 
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.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


-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se