[gmx-users] about pull_init and pull_start

zhongjin zhongjin1000 at yahoo.com.cn
Wed Sep 29 04:43:38 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 = 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


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