[gmx-users] about pull_init and pull_start

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 29 04:57:47 CEST 2010

zhongjin wrote:
> 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=

Hooke's Law.

> 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
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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