[gmx-users] Umbrella sampling
ndhumal at andrew.cmu.edu
Sat Jan 1 16:11:06 CET 2011
I am trying to run umbrella sampling for my system. I have system with
four ion pair (cation and anion) of ionic liquids and 2048 water
molecules. I am trying to PMF calculation with cation-anion distance as a
reaction coordinate. I choose cation as group1 and anion group2.
Box dimensions are 39.222 39.222 39.222 90 90 90
Durinh equilibratation cation and anion gets dissociate and move far from
each other (around 7-8 A). Both cation and anion are close to edges of the
box. I am more interested in structure where cation and anion close
(around 2-4A).How can I do the PMF simulation to get this structure. Can I
define pull_rate1 = -0.01 to get cation and anion to get close.
How can I keep cation and anion at center or if they close to the box
edges then does the periodic images of the system will interact?
Down I pasted the part of pull code used in my.mdp file.
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = YES ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = EMI
pull_group1 = ETS
pull_init1 = 0.0
pull_rate1 = -0.01 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000 ; kJ mol^-1 nm^-2
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