Qian Wang wrote:
Hi,
I want to use pulling code. But I do not quite sure the meaning of
pull_rate. User guide saies this is the rate of change of the reference
position. So if I set this value to 0.0001, does it mean the reference
postion will move 0.0001 nm/ps ? If yes, how to define the moving
direction? Generally speaking, how to choose the value for this
parameter? Thanks very much.
The pull_rate parameter is the velocity of the biasing force, in the case of a
harmonic potential, for instance, this is the velocity at which the spring
moves, not necessarily the velocity at which the pull group is being moved,
based on the evolution of the forces. The pull_vec1 parameter sets the vector
along which the force is applied.
As for the pull rate, that is a complicated question. You need to pull fast
enough to make the simulation feasible, but slow enough such that you do not
significantly perturb the dynamics, i.e., a sudden, sharp pull that violently
abstracts your pulled group :) There is plenty of literature out there with
regards to pulling. I'd suggest you do some reading. You can do some of your
own testing by using several pull rates and examining the effect the rate has on
the resulting trajectories.
-Justin
Qian
--
========================================
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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