[gmx-users] Umbrella sampling

Justin A. Lemkul jalemkul at vt.edu
Sat Jan 1 20:01:58 CET 2011

Nilesh Dhumal wrote:
> Hello
> 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?

You need to define a series of configurations along a pre-defined reaction 
coordinate to properly do umbrella sampling.  Whether or not you can converge 
four independent pairs is questionable, but I've never tried it.  I think I've 
said this before: simplify your system.  Start with one pair in water and see if 
you get a sensible answer and understand the workflow, then build your system up.

If your umbrella restraint distance is larger than half the smallest box vector 
in the pull dimension, the periodic distance is used instead of the distance 
directly across the unit cell.  Knowing whether or not the periodic distance 
will be used comes from proper planning - define the range of distances that 
will make up your reaction coordinate, then make your box at least twice as 
large (allowing some extra space for oscillation about your longest restraint 
distance and pressure coupling, if applicable).

All of the conceptual details are described in a tutorial I wrote.  It sounds to 
me like you're trying to generate a PMF from a single umbrella sampling window, 
which cannot be done.



> Down I pasted the part of pull code used in my.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      = -0.01          ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 1000          ; kJ mol^-1 nm^-2


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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