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

[Justin Lemkul]

On 9/4/14, 9:42 PM, Lyna Luo wrote:
> 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:
>
> job.job13.10.sort.colvars.traj,temp.pdo.gz
>
> 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:
>
> job.job13.0.sort.colvars.traj,temp.pdo.dat
>
> My pdo file format is:
>
> # UMBRELLA 3.0
>
> # 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!

Read the help description.  The -ip (and all other similar input options) 
require a .dat file, which is a simple text file that lists the file names.  You 
do not provide the actual file names themselves anywhere on the command line.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================