On 9/23/15 9:36 AM, Sepideh Kavousi wrote:
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 don't see how the constraint method relates to MSD.
A bigger box with the same length of reaction coordinate would avoid jumps
across PBC.
-Justin
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 <jalem...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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