Dear Gromacs users,
I've run the umbrella sampling. I could draw histograms with sufficient
overlap, so I determined all of the simulations reached enough length of
time. Now it's the analysis step.
When I chose tpr files and pullf.xvg (forces) files as the input to
wham, I was able to analyze and draw PMF curve previously.
However, I chose tpr files and pullx.xvg (coordinates) files, I couldn't.
The command line is below.
gmx wham -it tpr-files.dat -ix pullx-files.dat -o -hist -unit kCal -b 50000 -e
200000
I got the profile.xvg but all PMF values are zero in that file.
While running gmx wham, I was getting warnings like below.
Warning, poor sampling bin 199 (z=-1.00185). Check your histograms!
I did simulation by using following COM pulling options:
; COM PULLING
pull = umbrella
pull_geometry = cylinder
pull_dim = N N Y
pull_r1 = 2
pull_r0 = 3
pull_constr_tol = 1e-06
pull_start = yes
pull_nstxout = 100
pull_nstfout = 100
pull_ngroups = 2
pull-ncoords = 1
pull-group1-name = zpopc
pull-group2-name = Protein
pull-coord1-groups = 1 2
pull-coord1-origin = 0 0 0
pull-coord1-vec = 0 0 -1.0
pull-coord1-init = 0
pull-coord1-rate = 0
pull-coord1-k = 1000
pull-coord1-kB = 0
Please help me in this regard.
Many Thanks
Misa Banno
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