[gmx-users] no data read from file pdo.gz

[Lyna Luo]

Hi Justin,

The blank between lines are just from email format. I used only one window to see if g_wham can readin my data, but I actually have 64 window. Please see the error message below. Thanks again! -Lyna


GROMACS:      gmx wham, VERSION 5.0

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

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

Command line:

  g_wham -ip pdo.dat -bins 400 -temp 300 -tol 0.00001 -auto


Found 64 pdo files in pdo.dat

Automatic determination of boundaries from 64 pdo files...

Using gunzig executable /bin/gunzip

Opening disa_job13_pdo/job.job13.63.sort.colvars.traj,temp.bb.pdo.gz ... [100%]


Determined boundaries to 100000002004087734272.000000 and -100000002004087734272.000000


Opening disa_job13_pdo/job.job13.0.sort.colvars.traj,temp.bb.pdo.gz ... [ 2%]

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

Opening disa_job13_pdo/job.job13.1.sort.colvars.traj,temp.bb.pdo.gz ... [ 3%]

WARNING, no data points read from file disa_job13_pdo/job.job13.1.sort.colvars.traj,temp.bb.pdo.gz (check -b option)

Opening disa_job13_pdo/job.job13.2.sort.colvars.traj,temp.bb.pdo.gz ... [ 5%]

WARNING, no data points read from file disa_job13_pdo/job.job13.2.sort.colvars.traj,temp.bb.pdo.gz (check -b option)


My pdo file looks like below. Is there something wrong with "component selection" or "nskip" or the two column data format?

# UMBRELLA 3.0

# Component selection: 0 0 1

# nSkip 1

# Ref. Group TestAtom

# Nr. of pull groups 1

# Group 1 GR1 Umb. Pos. 57.6 Umb. Cons. 2.0

#####

5054910 5.76202567601903e+01

5054920 5.76153109776819e+01

5054930 5.76057280906502e+01

5054940 5.76000707360825e+01

5054950 5.75956747536078e+01

5054960 5.75863624004517e+01

5054970 5.75807826101227e+01

5054980 5.75752353578918e+01

5054990 5.75700050629966e+01

5055000 5.75644906348954e+01

5055010 5.75599694771144e+01

5055020 5.75577873701180e+01

5055030 5.75528304157033e+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: Sunday, September 7, 2014 at 11:58 AM
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] no data read from file pdo.gz



On 9/7/14 2:37 AM, Lyna Luo wrote:
Dear GMX experts,

I can not figure out how to make g_wham readin data from my pdo file below, even though I tried different -b option and component selections. Please see the error message below. Thank you so much! -L

# 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


I don't know if this is a consequence of the email or it's the actual format of
the .pdo file, but there are skipped lines between everything that will cause
incorrect interpretation of contents.  Though if there were really a problem,
there should be a fatal error, so I'm not 100% sure if this is a problem.



GROMACS:      gmx wham, VERSION 5.0

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

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

Command line:

    g_wham -ip tt.dat -bins 5 -temp 300 -tol 0.001 -auto


Found 1 pdo files in tt.dat

A single .pdo file corresponds to a single window.  You can't build a reaction
coordinate from a single sampling window, so basically everything after this
point is total junk.

-Justin


Automatic determination of boundaries from 1 pdo files...

Using gunzig executable /bin/gunzip

Opening test.pdo.gz ... [100%]


Determined boundaries to 100000002004087734272.000000 and -100000002004087734272.000000


Opening test.pdo.gz ... [100%]

WARNING, no data points read from file test.pdo.gz (check -b option)



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

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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