[gmx-users] about pull_init and pull_start
Justin A. Lemkul
jalemkul at vt.edu
Wed Sep 29 04:57:47 CEST 2010
> Hi all, I am sorry to ask such a question,may it seems very stupid, but I am
> very confused about it. pull_init is the reference distance at t=0. the
> reference distance is the distance between the pull group and the reference
> group? This is a single value, except for geometry position which uses a
> vector.If it is a single value,it can be negative or positive? pull_start =
By definition, a distance (a scalar quantity) must be positive.
> yes,add the COM distance of the starting conformation to pull_init. What it
> means? I have seen from somewhere else :Setting pull_start = yes means that
> the initial COM distance is the reference distance, and we do not have to
> define a reference (pull_init1) separately for each configuration. How is the
Correct. It's an easy way out. Using "pull_start = yes" + "pull_init1 = 0"
means that the initial COM distance (whatever it is) is the reference distance.
The equivalent could be accomplished by using "pull_start = no" + "pull_init1
= (COM distance)"
> pulling force caculated? My case may be a little special, I want to use pull=
> umbrella,pull_geometry = distance ,but my pull group is very close to
> reference group ,the Z coordinate of COM of reference group is 1.81939,1.822
> for COM of pull group. I came across a problem :Pull reference distance for
> group 1 is negative (-0.000020)
You've answered your own question from above without even asking it on the list.
You're getting a negative distance, and hence an error. I don't know what
settings you're using, but "pull_start = yes" + "pull_init1 = 0" should (in
theory) solve the issue.
> Zhongjin He
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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