cmsuser
November 20, 2020, 7:12pm
1
GROMACS version:2018.2-gcc910
I found the following problem when I do umbrella sampling calculation.
When I do WHAM, it says it switched to exact iteration and the output in hist.xvg shows all the energies are zero.
What could be wrong? I am doing PMF calculation of pulling two slabs of polymers apart. I imagine the force could be very large.
Any comments or suggestions would be appreciated.
"Wrote histo.xvg
1) Maximum change 2.864556e+02
100) Maximum change 7.539510e-01
200) Maximum change 7.172030e-01
300) Maximum change 1.411430e+00
Switched to exact iteration in iteration 303
hist.xvg should have multiple histograms of positions within each window along the reaction coordinate, not energies. Do you get any overlap between these histograms? They should not be all zero, as some sampling had to occur somewhere.
cmsuser
November 24, 2020, 2:10pm
3
My hist.xvg is actually the PMF output file. They have all zeros.
This file was created Fri Nov 20 11:48:34 2020
Created by:
:-) GROMACS - gmx wham, 2018.2 (-:
Executable: /share/apps/gromacs/2018.2/bin/gmx_mpi
Data prefix: /share/apps/gromacs/2018.2
Working dir: /home/**/umbrella_sampling2
Command line:
gmx_mpi wham -it tpr-files.dat -if pull-files.dat -o hist -unit kT
gmx wham is part of G R O M A C S:
Good gRace! Old Maple Actually Chews Slate
@ title “Umbrella potential”@TYPE xy