[gmx-users] Re: pre-wham

[lloyd riggs]

If I just make a sub directory and move every fill (.tpr, pullf.xvg, etc... it works, so must not be gromacs realted I appologise)

Stephan Watkins

-------- Original-Nachricht --------
> Datum: Mon, 16 Apr 2012 15:35:17 +0200
> Von: "lloyd riggs" <lloyd.riggs at gmx.ch>
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Betreff: [gmx-users] Re: pre-wham

> 
> Dear all,
> 
> Im using wham on series of runs and have run into the following proble.
> 
> The command line 
> 
> >g_wham_d -if pullf.dat -it tpr.dat -temp 300 -o whamf.xvg -hist outf.hist
> -unit kCal
> 
> will work in one run, but not the next one as I go through I found a
> couple that give the error
> 
> Fatal error:
> Found 1 pull groups in traj_4.tpr,
>  but 2 data columns in pullf.xvg (expected 1)
> 
> if I remove the time column, then it asks for two columns.  I get the same
> thing from the pullx.
> 
> now, I have looked and looked and can not find a problem in anything.  All
> the .tpr files were generated from a template file the same, all the
> outputs look the same and have the same format and positions down to tab
> spacing, and the input files (Dat files) are simple one lines pullf.xvg, pullx.xvg
> or #.tpr.  This one is driving me batty as I cant find an inconsistency
> but have an inconsitent error message.
> 
> This is around only a couple runs, and I was going over each one
> individually with wham, before the generalized mass submission to wham for error
> bars and gaussien.  The ones that work give nice curves and are relativly
> close in output, the pullf and pullx of the ones that work and dont are
> realitve as well?  Any suggestions before I go batty are appriciated.
> 
> Sincerely,
> 
> Stephan Watkins
> 
> An example pullf or pull x file
> 
> ________________
> @    title "Pull COM"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "Position (nm)"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "0 Y"
> @ s1 legend "1 dY"
> 0.0000	5.46393	5.31908
> 2.0000	5.47052	5.34938
> 4.0000	5.46465	5.3283
> 6.0000	5.46107	5.3163
> 8.0000	5.46298	5.31637
> ...
> 
> or 
> 
> #
> # mdrun_mpi_d is part of G R O M A C S:
> #
> # GROningen MAchine for Chemical Simulation
> #
> @    title "Pull force"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "Force (kJ/mol/nm)"
> @TYPE xy
> 0.0000	-7.99361e-11
> 2.0000	58.602
> 4.0000	14.4378
> 6.0000	11.5715
> 8.0000	13.4292
> 10.0000	31.9026
> 12.0000	28.7603
> 14.0000	25.9416
> ....
> 
> 
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