[gmx-users] Problem with trjcat -demux

[Justin A. Lemkul]

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
>>
> 
> 

-- 
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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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