[gmx-users] REMD trjcat -demux problem

David van der Spoel spoel at xray.bmc.uu.se
Wed Aug 20 08:28:13 CEST 2008

Di Pan wrote:
> Hi, everyone:
> I met a problem when I try to use the trjcat -demux to connect 
> trajectory files of REMD. I use 68 replicas for REMD simulation, and use 
> demux.pl script to get the replica_index.vgx file. Then I try to use the 
> trjcat -f traj*.xtc -demux replica_index.xvg to get a continuous 
> trajctory file. But I got an error information as below:
> Fatal error:
> Demuxing the same replica 2 twice at time 32.000000
> My REMD sets the exchange time at every 2ps and record the coordinate 
> information also at every 2ps.

Check the index file at the line corresponding to 32 ps. Does it have 
the number 2 more than once?
Was the index file meddled with, maybe transported from one computer to 

> Does anyone meet the same problem or can give me some advice? I much 
> appreciate any advice and help.
> Di,Pan
> Graduate Student at
> School of Engineering
> Department of Biomedical Engineering
> University of Alabama at Birmingham
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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