[gmx-users] g_wham error
Justin A. Lemkul
jalemkul at vt.edu
Tue Mar 16 21:45:53 CET 2010
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.
> 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
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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