[gmx-users] Problem with trjcat -demux

[Justin A. Lemkul]

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

========================================