[gmx-users] Umbrella sampling

[Nilesh Dhumal]

Hello
I am trying to run umbrella sampling for my system. I have system with
four ion pairs (4 cation and 4 anion) of ionic liquids and 1024 water
molecules. I am trying to PMF calculation with cation-anion distance as a
reaction coordinate.  I choose cation as group1 and anion group2.
I am getting the free energy around ~400 kcal.  Can you tell where I am
going wrong?

I have one more question, In my equilibrated strcutrue cations and anions
are far from each other (around 7-8 A). 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.
I have pasted pull code used in mdp file.

Nilesh


; 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      = 0.001          ; 0.01 nm per ps = 10 nm per ns
pull_k1         = 1000          ; kJ mol^-1 nm^-2