Gavin Melaugh wrote:
Hi Justin
Thanks. If I use the pull_geometry = direction I would go for the
following jus t to pull the molecules together in the z direction.
pull = umbrella
pull_geometry = direction
pull_start = yes
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = cage_2
pull_vec1 = 0.0 0.0 -1.0
pull_rate1 = 0.01
pull_k1 = 1000
Does this seem reasonable? Also in the pull_rate what is meant by the
Probably. Try it.
'rate of change of the reference position'? (Is it the position of the
reference group, if so what if I don't want it to change?)
It is the rate of change of the reference position, which is the position at the
outset of the simulation. Your objective is to pull your two species together,
right? I don't see why you wouldn't want it to change. You're not changing
anything about pull_group0 (your reference group), since you aren't setting
pull_rate0. Everything is applied to pull_group1 (hence _rate1, _k1, etc).
-Justin
Cheers
Gavin
--
========================================
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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