[gmx-users] Re: pre-wham

lloyd riggs lloyd.riggs at gmx.ch
Mon Apr 16 15:35:17 CEST 2012

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.


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


# 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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