[gmx-users] problem with variable fio in REMD

[Justin A. Lemkul]

Rebeca García Fandiño wrote:
> Hello,
> I am trying to do Replica Exchange with 50 replicas, but I am having 
> problems when using trjcat with -demux.
>  
> trjcat -f mdA_0.xtc mdA_1.xtc mdA_2.xtc mdA_3.xtc mdA_4.xtc mdA_5.xtc 
> mdA_6.xtc mdA_7.xtc mdA_8.xtc mdA_9.xtc mdA_10.xtc mdA_11.xtc mdA_12.xtc 
> mdA_13.xtc mdA_14.xtc mdA_15.xtc mdA_16.xtc mdA_17.xtc mdA_18.xtc 
> mdA_19.xtc mdA_20.xtc mdA_21.xtc mdA_22.xtc mdA_23.xtc mdA_24.xtc 
> mdA_25.xtc mdA_26.xtc mdA_27.xtc mdA_28.xtc mdA_29.xtc mdA_30.xtc 
> mdA_31.xtc mdA_32.xtc mdA_33.xtc mdA_34.xtc mdA_35.xtc mdA_36.xtc 
> mdA_37.xtc mdA_38.xtc mdA_39.xtc mdA_40.xtc mdA_41.xtc mdA_42.xtc 
> mdA_43.xtc mdA_44.xtc mdA_45.xtc mdA_46.xtc mdA_47.xtc mdA_48.xtc 
> mdA_49.xtc -o trajout_A.xtc -demux replica_index.xvg
>  
> I get the replica_index.xvg from demux.pl mdA_0.log. The calculation 
> finishes with this error:
>  
> 
> Read 50 sets of 500 points, dt = 2
> 
> Reading frame     300 time   12.000
> -------------------------------------------------------
> Program trjcat, VERSION 3.3.99_development_20080718
> Source code file: gmxfio.c, line: 822
> 
> Range checking error:
> Variable fio has value 268369076. It should have been within [ 0 .. 51 ]
> 
> -------------------------------------------------------

Specify multiple output file names.  Also, you should probably upgrade to the 
newest official version, instead of using an old CVS version.  That way, you'll 
get the newest features and bug fixes.

> 
> I have found an error analogous to this in the mail archive (http://www.mail-archive.com/gmx-users@gromacs.org/msg18278.html), but it is unresolved.
> 

I reported this same error as a bug.  The upcoming version (4.0.4) should 
contain a fix that will automatically generate multiple output files from a 
single -o filename.

-Justin

> Please, could anyone help me?
> 
> Thank you very much,
> 
>  
> 
> Rebeca García
> 
> Parc Cientific de Barcelona
> 
> regafan at hotmail.com <mailto:regafan at hotmail.com>
> 
> 
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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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