[gmx-users] PMF calculation_ Constraint

[Justin Lemkul]

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

==================================================