[gmx-users] Umbrella Sampling - good histogram but no result in profile

Ben Tam btam125 at hotmail.co.uk
Wed Mar 14 15:44:11 CET 2018

Dear all,

I have a rather strange problem. Currently I am trying to get a PMF of a water molecule through a hydrophobic materials. At the end of using "gmx wham", I get a rather good histogram and it cover the whole range of the system. However at the making profile.xvg. I get the answer "nan" inside the file. Therefore I really cannot think of why is it giving me that?

Currently I set it as :
;Pull code
pull = yes
;pull-cylinder-r = 0.5
pull_ngroups = 2
pull_ncoords = 1
pull_group1_name = SOL
pull_group2_name = MOL
pull_coord1_type = umbrella ; harmonic biasing force
pull_coord1_geometry = direction-periodic ; simple distance increase, direction-periodic
pull_coord1_vec = 1 1 1
pull_coord1_groups = 1 2
pull_coord1_dim = Y Y Y
pull_coord1_rate = 0.00 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 10000 ; kJ mol^-1 nm^-2
pull_coord1_start = yes ; define initial COM distance > 0

Also this appears when I used the command "gmx wham":

Switched to exact iteration in iteration 1
           1) Maximum change -1.000000e+20
Converged in 2 iterations. Final maximum change -1e+20

Therefore I really don't understand what I have to do in order to get a profile.xvg. I understand the k value is high, but without that high value, the water won't settle within the assign window.

Am I doing something wrong? because I got a good histogram but no result in the profile.xvg? Thank you very much for your help.

Best regards,


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