[gmx-users] about pull_init and pull_start

[zhongjin]

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 = 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 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)

Zhongjin He

[Justin A. Lemkul]

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

Yes.

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.

-Justin

Zhongjin He

--
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | [phone]
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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