I followed up by trying trjcat version 3.3.3, which I have installed in a
different location. By issuing the same command, it gives another (different)
error:
Read 9 sets of 500 points, dt = 2
Reading frame 130 time 30.000
-------------------------------------------------------
Program trjcat_3.3.3_s, VERSION 3.3.3
Source code file: gmx_trjcat.c, line: 296
Fatal error:
Demuxing the same replica 4 twice at time 30.000002
-------------------------------------------------------
I found that this issue had been reported in the archive:
http://www.gromacs.org/pipermail/gmx-users/2008-August/035881.html
Unfortunately, there was no reply to David's inquiry in that thread, so I don't
know if a resolution was ever found. When I looked at the replica_index.xvg,
the line corresponding to 30 ps looks normal to me:
30 4 0 1 3 5 2 6 7 8
None of the numbers are repeated, and the file was created and is being used on
the same machine, so I have not manipulated it in any way.
Any ideas what might be going on here? It appears that version 3.3.3 proceeds
further than 4.0.2, without the fio error I previously reported.
Thanks for your time.
-Justin
Justin A. Lemkul wrote:
David van der Spoel wrote:
Justin A. Lemkul wrote:
Hi all,
I've just begun some work with REMD using Gromacs-4.0.2; it is my
first real attempt at doing REMD, so I'm trying to learn the correct
procedure. At the end of the simulations (9 replicates @ 1ns each,
just a quick test of how everything works), I want to try to assemble
continuous trajectories using trjcat -demux. The demux.pl script
worked to give me the two necessary index files. Following the
information on the wiki, I tried the following:
trjcat -f ../*.xtc -demux ../replica_index.xvg
Do you have the same number of xtcs as columns in the xvg file?
Yes. The leftmost column should be the time (ps), correct? Then I have
nine columns, corresponding to the nine replicas that I simulated:
0 0 1 2 3 4 5 6 7 8
2 0 1 2 3 4 5 7 6 8
4 0 1 2 4 3 7 5 6 8
6 0 1 4 2 3 7 6 5 8
8 0 1 4 3 2 7 6 5 8
10 0 1 4 3 2 7 5 6 8
...
-Justin
I got the following error:
Read 9 sets of 500 points, dt = 2
Reading frame 120 time 28.000
-------------------------------------------------------
Program trjcat_4.0.2_s, VERSION 4.0.2
Source code file: gmxfio.c, line: 938
Range checking error:
Variable fio has value 13691. It should have been within [ 0 .. 10 ]
-------------------------------------------------------
Have I done something wrong, or is there a problem in trjcat?
Thanks for your attention.
-Justin
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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