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

[Norfarisha Mohd Fadil]

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?


With thanks and regards,


Norfarisha binti Mohd Fadil

Student

Department of Chemistry
Faculty of Science
UTM, Johor Bahru
Malaysia