[gmx-users] Umbrella sampling

Nilesh Dhumal 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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