[gmx-users] Error with g_wham reading .pdo files

Lyna Luo luoy at westernu.edu
Fri Sep 5 04:15:25 CEST 2014

Dear gmx experts,

I'm using g_wham version 5.0 to generate PMF from non-gromacs umbrella sampling.
Following the option -ip, I prepared all pdo files in one directory  and gzip them.
Then I run "g_wham -v -ip *.gz -bins 400 -temp 300 -tol 0.00001 -auto". The output shows:

GROMACS:      gmx wham, VERSION 5.0

Executable:   /usr/local/gromacs/bin/gmx

Library dir:  /usr/local/gromacs/share/gromacs/top

Command line:

  g_wham -v -ip job.job13.0.sort.colvars.traj,temp.pdo.gz job.job13.10.sort.colvars.traj,temp.pdo.gz job.job13.11.sort.colvars.traj,temp.pdo.gz job.job13.12.sort.colvars.traj,temp.pdo.gz job.job13.13.sort.colvars.traj,temp.pdo.gz job.job13.14.sort.colvars.traj,temp.pdo.gz job.job13.15.sort.colvars.traj,temp.pdo.gz job.job13.16.sort.colvars.traj,temp.pdo.gz job.job13.17.sort.colvars.traj,temp.pdo.gz job.job13.18.sort.colvars.traj,temp.pdo.gz job.job13.19.sort.colvars.traj,temp.pdo.gz job.job13.1.sort.colvars.traj,temp.pdo.gz job.job13.61.sort.colvars.traj,temp.pdo.gz job.job13.62.sort.colvars.traj,temp.pdo.gz job.job13.63.sort.colvars.traj,temp.pdo.gz job.job13.6.sort.colvars.traj,temp.pdo.gz job.job13.7.sort.colvars.traj,temp.pdo.gz job.job13.8.sort.colvars.traj,temp.pdo.gz job.job13.9.sort.colvars.traj,temp.pdo.gz -bins 400 -temp 300 -tol 0.00001 -auto


Program g_wham, VERSION 5.0

Source code file: /root/gromacs-5.0/src/gromacs/commandline/pargs.cpp, line: 874

Invalid command line argument:


For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

If I run single pdo file, it shows different error message:

Command line:

  g_wham -v -ip job.job13.0.sort.colvars.traj,temp.pdo.gz -bins 400 -temp 300 -tol 0.00001 -auto


Program g_wham, VERSION 5.0

Source code file: /root/gromacs-5.0/src/gromacs/fileio/futil.cpp, line: 540

File input/output error:


My pdo file format is:


# Component selection: 0 0 1

# nSkip 1

# Ref. Group TestAtom

# Nr. of pull groups 1

# Group 1 GR1 Umb. Pos. 0 Umb. Cons. 2.0


     5054910    6.86778783227709e-01

     5054920    7.12201410957491e-01

     5054930    7.20695103841784e-01

     5054940    7.10706445794138e-01

     5054950    7.30693655979543e-01

     5054960    7.33930839499955e-01

     5054970    7.45784725425651e-01

     5054980    7.66841219351832e-01

     5054990    7.61835548305989e-01

     5055000    7.69643361420997e-01

Is my pdo file format right? What is the correct way to use g_wham -ip option? Thank you!

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