[gmx-users] Umbrella Sampling, Analysis Step

[Misa Banno]

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