[gmx-users] PMF calculation with constraint distance
leilasalimi at gmail.com
Thu May 21 23:00:05 CEST 2015
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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