[gmx-users] demixing REMD trajectories

David van der Spoel spoel at xray.bmc.uu.se
Mon Feb 25 07:49:50 CET 2008

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 

> 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
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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

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