[gmx-users] umbrella sampling with "pull=constraint"

Vijayaraj vijayaraj81 at gmail.com
Mon Nov 7 14:30:25 CET 2011


I have done umbrella sampling with "pull=umbrella" and I found that the
pulling group has high fluctuations and sometimes moving out of the
periodic box. I think that the harmonic potential is not properly applied
and thus the pulling group is not retained with the specified COM distance
between the reference and pulling group. Can we use pull=constraint option
to retain the pulling group within the COM distance? my pulling code is as
bellow with restrain at 0.5nm distance from ref group. I just want to get
some idea about this pull code modification.

pull            = constraint
pull_geometry    = distance
pull_dim        = N N Y
pull_start      = no
pull_ngroups    = 1
pull_group0     = Chain_A
pull_group1     = Chain_B
pull_init1      = 0.50
pull_rate1      = 0.0
pull_k1         = 1000
pull_nstxout    = 500
pull_nstfout    = 500

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