[gmx-users] g_wham error

[Justin A. Lemkul]

Gard Nelson wrote:
> Here's my .xvg:
> 
> # This file was created Mon Mar  8 01:50:07 2010
> # by the following command:
> # /opt/apps/intel10_1/mvapich1_1_0_1/gromacs/4.0.5/bin/mdrun_mpi -multi 
> 31 -deffnm onePREP -px onePREP -np 2976 -maxh 3
> #
> # /opt/apps/intel10_1/mvapich1_1_0_1/gromacs/4.0.5/bin/mdrun_mpi is part 
> of G R O M A C S:
> #
> # Great Red Oystrich Makes All Chemists Sane
> #
> @    title "Pull force"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "Force (kJ/mol/nm)"
> @TYPE xy
> 0.0000  -0.000538731
> 2.0000  -104.01
> 4.0000  -128.037
> 6.0000  29.3498
> 8.0000  6.12135
> 10.0000 142.886
> 12.0000 141.699
> 
> So why would I only be getting the one data column instead of the 
> expected 6? 
> 
> onePREP0.xvg is a pullx file.  The command I use is:
> 

Based on its contents, no it's not.  Note that the data contained therein are 
forces.  A pullx.xvg file should have coordinates - x, y, z for both reference 
and pull group, hence six columns, in addition to the time column.

> g_wham -ix PREPxvg.dat -it PREPtpr.dat
> 
> PREPxvg.dat and PREPtpr.dat are lists of the respective xvg and tpr 
> files.  They are both in the same order, although they are ordered 
> alphabetically instead of sequentially (i'm not sure if that matters or 
> not).  Here's PREPxvg.dat to illustrate the ordering:
> 

Order is all that matters, as far as I am aware.

-Justin

> onePREP0.xvg   onePREP16.xvg  onePREP22.xvg  onePREP29.xvg  onePREP7.xvg
> onePREP10.xvg  onePREP17.xvg  onePREP23.xvg  onePREP2.xvg   onePREP8.xvg
> onePREP11.xvg  onePREP18.xvg  onePREP24.xvg  onePREP30.xvg  onePREP9.xvg
> onePREP12.xvg  onePREP19.xvg  onePREP25.xvg  onePREP3.xvg
> onePREP13.xvg  onePREP1.xvg   onePREP26.xvg  onePREP4.xvg
> onePREP14.xvg  onePREP20.xvg  onePREP27.xvg  onePREP5.xvg
> onePREP15.xvg  onePREP21.xvg  onePREP28.xvg  onePREP6.xvg
> 
> Thanks for the help
> Gard
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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