[gmx-users] Umbrella Sampling with water molecules flying away from the reference point

Ben Tam btam125 at hotmail.co.uk
Thu Apr 19 12:03:20 CEST 2018

Dear GROMACS users,

Currently I am experiencing a problem. At the moment I am trying to do a umbrella sampling with water going through a porous material. I have generate the configuration based on CV direction (1,1,1).

However when I watch the movie back for individual simulation. I see the water molecules fly beyond the area where I want to sample. I have tried using flat bottom potential on the water molecule and increasing k value up to 500,000 kJ mol-1, but it still flying away. Hence can any body suggest me how to solve this?

Now I am wondering, how does the umbrella sampling does the job? because after all this simulation, now I doubting that the spring potential applied at water Center of Mass position. In the movie file, it seems to me that the spring potential are attached to the Center of Mass of the whole system (water and the porous material), I hope I am wrong here. I have double check my index file as well and there isn't any naming error.

The input for the pull file as follow:

;Pull code

pull = yes
;pull_cylinder_r = 0.5
pull-ngroups = 2
pull-ncoords = 1
pull-group1-name = water
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 = 25000 ; kJ mol^-1 nm^-2
pull-coord1-start = yes ; define initial COM distance > 0

Thank you very much.

Best regards,


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