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

[Lyna Luo]

Thank you so much. I fixed the problem #1. But my pdo format file still has problem.

Command line:

  g_wham -ip tt.dat -bins 10 -temp 300 -auto -tol 0.0001 -b 5055


Found 1 pdo files in tt.dat

Automatic determination of boundaries from 1 pdo files...

Using gunzig executable /bin/gunzip

Opening disa_job13_pdo/job.job13.0.sort.colvars.traj,temp.pdo.gz ... [100%]


Determined boundaries to 100000002004087734272.000000 and -100000002004087734272.000000


Opening disa_job13_pdo/job.job13.0.sort.colvars.traj,temp.pdo.gz ... [100%]

WARNING, no data points read from file disa_job13_pdo/job.job13.0.sort.colvars.traj,temp.pdo.gz (check -b option)



Back Off! I just backed up histo.xvg to ./#histo.xvg.4#

Wrote histo.xvg

Getting initial potential by integration.


WARNING, no data point in bin 0 (z=9e+19) !

You may not get a reasonable profile. Check your histograms!


Am I using the right component selection for time column and one data column (I assume it means x y z)? Thanks!


# 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

From: Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>>
Reply-To: "gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>" <gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>>
Date: Thursday, September 4, 2014 at 7:35 PM
To: "gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>" <gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>>
Subject: Re: [gmx-users] Error with g_wham reading .pdo files



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

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