[gmx-users] demixing REMD trajectories

madeleine.kittner at mpikg.mpg.de madeleine.kittner at mpikg.mpg.de
Mon Feb 25 02:20:36 CET 2008

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
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.

Thanks for your help.


Madeleine Kittner, PhD student
Department of Theory and Bio-Systems
Max Planck Institute of Colloids and Interfaces
Research Campus Golm
14424 Potsdam, Germany

More information about the gromacs.org_gmx-users mailing list