[gmx-users] Umbrella sampling using 3-dimensions

Mirijanian, Dina Tigranui dtmirij at sandia.gov
Thu Mar 13 21:52:59 CET 2008

Hello everyone,

I would like to clarify exactly what is restrained in a simulation when
doing umbrella sampling, using  "pulldim = Y Y Y"  in the .ppa input file.

Consider you have the following in the .ppa file:

verbose                  = no
runtype                  = umbrella
ngroups                  = 1
group_1                  = B
reference_group          = A
reftype                  = com
reflag                   = 1
pulldim                  = Y Y Y
k1                       = 1000
pos1                     = 1.5 2.5 7.0

The output .pdo file will give three columns of output, one for x , y and z
What I need clarified is whether, in a simulation demonstrated above, it is
the DISTANCE of the vector between the center-of-mass of group A and B that
is being restrained or the actual vector with each component being
restrained itself. i.e., is the umbrella restraining force being applied on
the DISTANCE or the actual vector.
I found this question was asked in a previous post but was not answered.

Thank you.

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