[gmx-users] PMF calculation with constraint distance

leila salimi leilasalimi at gmail.com
Thu May 21 23:00:05 CEST 2015

Hi all,

I started to calculate PMF between two ions in solution and I
used constraint for pull option, instead of umbrella as I saw in Umbrella
sampling Tutorial of Justin.

This is the part of my mdp file!
; Pull code
pull            = constraint    ; Justin's value was "umbrella"
pull_geometry   = distance      ; simple distance increase
pull_dim        = Y Y Y
pull_start      = no            ; Justin's value was "yes"
pull_ngroups    = 1
pull_group0     = CA_surf
pull_group1     = carboxylate_carbon
pull_init1      = 0.288         ; initial distance between pulling groups
pull_rate1      = 0.001 ; 0.001 nm per ps
pull_k1         = 1000          ; kJ mol^-1 nm^-2

I got the output  and I tried to pull out with increasing  the distance
between two atoms and I have pullf.xvg file!

I know that I can have the time evolution of constrained distance with
g_dist from xtc file! I am wondering how to have the distance with
corresponding constrained force?
If I have the file contain forces and distances, I can integrate the force
then I will have PMF.

Could you help me that how I can manage this?

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