[gmx-users] Umbrella sampling

[Nilesh Dhumal]

 Justin,
I considered single ion- pair.
sorry for typing mistake (I wrote 4 ion-pairs).

How can I define distance range.
ONe more my cation and anion are close in box edges in my equilibrated
strucutre.

By defining pull_rate1      = -0.01 can cation and anion will come close
to each other?

Nilesh


Does will it affect on results?

On Sat, January 1, 2011 2:01 pm, Justin A. Lemkul wrote:
>

>
> 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.
>
> http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sam
> pling
>
> -Justin
>
>
>> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
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