[gmx-users] Unable to generate umbrella histogram and PMF curve

[Justin Lemkul]

On 6/19/17 8:52 PM, Norfarisha Mohd Fadil wrote:
> Dear users,
> 
> 
> I ran a WHAM analysis after umbrella sampling simulation, and this error occurred:
> 
> 
> Reading pull force file with pull geometry distance and 1 pull dimensions
> Expecting these columns in pull file:
>      0 reference columns for each individual pull coordinate
>      1 data columns for each pull coordinate
> With 1 pull groups, expect 2 columns (including the time column)
> Reading file umbrella1.tpr, VERSION 5.1.4-dev (single precision)
> Reading file umbrella2.tpr, VERSION 5.1.4-dev (single precision)
> Reading file umbrella3.tpr, VERSION 5.1.4-dev (single precision)
> Reading file umbrella4.tpr, VERSION 5.1.4-dev (single precision)
> Reading file umbrella5.tpr, VERSION 5.1.4-dev (single precision)
> Reading file umbrella6.tpr, VERSION 5.1.4-dev (single precision)
> Reading file umbrella7.tpr, VERSION 5.1.4-dev (single precision)
> Reading file umbrella8.tpr, VERSION 5.1.4-dev (single precision)
> Reading file umbrella9.tpr, VERSION 5.1.4-dev (single precision)
> Reading file umbrella10.tpr, VERSION 5.1.4-dev (single precision)
> Reading file umbrella11.tpr, VERSION 5.1.4-dev (single precision)
> Reading file umbrella12.tpr, VERSION 5.1.4-dev (single precision)
> 
> -------------------------------------------------------
> Program gmx wham, VERSION 5.1.4-dev
> Source code file: /home/biotech/Downloads/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp, line: 2240
> 
> Fatal error:
> Empty pull force file npt12_pullf.xvg
> 
> Why is the pull force file not generated for the particular xvg file? If the file is empty, then how should I fix it? Should I redo the umbrella sampling simulation?
> 

Inspect the contents of your files and try to figure out what happened.  An 
empty file suggests a failed run, which should be obvious based on the .log file.

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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