[gmx-users] umbrella sampling

Ben Tam btam125 at hotmail.co.uk
Tue Jul 11 18:09:53 CEST 2017

Dear All,

I am doing umbrella sampling for a water molecules moving inside a crystal structure, however I am running into a problem on the output file with profile.xvg all value showing “nan”. This error has occurred when I reduce the slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for 0.2 and 0.1, however only 0.2 has given me meaningful profile. The pull code I used is the following:

;Pull code
pull = yes
pull_ngroups = 2
pull_ncoords = 1
pull_group1_name = MOL
pull_group2_name = SOL
pull_coord1_type = umbrella ; harmonic biasing force
pull_coord1_geometry = distance ; simple distance increase
;pull_coord1_vec = 0 0 1
pull_coord1_groups = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 10 ; kJ mol^-1 nm^-2
pull_coord1_start = yes ; define initial COM distance > 0

and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I have tried increasing the k value to 50 and 100 with the same results.

The histogram shows many overlap, however when I use k value 100, it is only giving me individual single peak. Therefore can someone enlighten on what is going on?

Best regards,


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