# [gmx-users] PMF calculation_ Constraint

Sepideh Kavousi skavou1 at tigers.lsu.edu
Wed Sep 23 15:36:56 CEST 2015

Dear Justin.
Thanks for response. I used constraint method because I wanted to calculate
MSD, How does using a bigger box helps me? because when  I make box bigger,
I need to run a little bit to equilibrate system, and again the tocopherol
can move and come out of the box.

On Tue, Sep 22, 2015 at 5:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/22/15 3:46 PM, Sepideh Kavousi wrote:
>
>> Dear Gromacs users
>>
>> I want to calculate the PMF of tocopherol in DMPC bilayer system. For this
>> means, I used Constraint method. the pull code in my .mdp file is :
>>
>> pull = constraint
>> pull-geometry = distance    ;distance, direction, or cylinder
>> pull-dim = N N Y
>> pull-constr-tol = 1e-6
>> pull-start = yes                    ;add current COM distance to
>> pull_init?
>> pull-print-reference = no
>> pull-nstxout = 10000
>> pull-nstfout = 5
>> pull-ngroups = 2
>> pull-ncoords = 1
>> pull-group1-name = DMPC
>> pull-group2-name = VIT
>> pull-coord1-groups = 1 2
>> pull-coord1-init = 0.0
>>
>>
>> In my output file which shows force over time, we have some sudden
>> diverges
>> of force to a very high number.
>> I realized it is because of the boundary condition, one part of molecule
>> comes out of the box and enters from the other side of the box and it
>> needs
>> a huge force to keep the molecule at the same position. Can you please
>> help
>> me how to solve this problem
>>
>>
> Use a bigger box, use a shorter reaction coordinate, or use an umbrella
> sampling method that supports PBC.  I suspect any output using the
> constraint method will be very poorly converged.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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