Dear Gromacs Users,
I am trying to study ligand unbinding adopting Umbrella sampling (using Gmx
4.5.3). during my initial pull to generate configurations for umbrella windows
I have pulled in the -Z direction,
@ s0 legend "0 Z"
@ s1 legend "1 dZ"
0.0000 7.37361 -0.33625
0.0200 7.37377 -0.33631
0.0400 7.37404 -0.33637
0.0600 7.3744 -0.33643
0.0800 7.37473 -0.33649
.
.
.
.
321.0800 7.37523 -1.29949
321.1000 7.37442 -1.29955
321.1200 7.37374 -1.29961
321.1400 7.37355 -1.29967
321.1600 7.37404 -1.29973
321.1800 7.37491 -1.29979
321.2000 7.3757 -1.29985
321.2200 7.37608 -1.29991
321.2400 7.37595 -1.29997
321.2600 7.37518 -1.30003
321.2800 7.37395 -1.30009
.
.
.(so on)
Now when I ran simulations in each umbrella windows, the PMF energies are in
negative. My guess is that this is due to my initial setup, or is there
something seriously wrong. And if i am right I should get the correct PMF by
taking the negative of this PMF (or is it)??
-----
; Pull code (pulling simulation)
pull = constraint
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = Protein
pull_group1 = MAL
pull_rate1 = 0.005 ;
pull_k1 = 1000 ; kJ mol^-1 nm^-2
pull_nstxout = 500 ; every 1 ps
pull_nstfout = 500 ; every 1 ps
-----
; Pull code (Umbrella simulation)
pull = umbrella
pull_geometry = distance ;
pull_dim = Y Y Y
pull_start = yes ;
pull_ngroups = 1
pull_group0 = Protein
pull_group1 = MAL
pull_rate1 = 0.000 ;
pull_k1 = 1000 ; kJ mol^-1 nm^-2
pull_nstxout = 500 ; every 1 ps
pull_nstfout = 500 ; every 1 ps
Best,
nahren
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