[gmx-users] oscillations in constrain forces

fangel at usc.es fangel at usc.es
Mon Jun 21 11:21:11 CEST 2004

Dear all,
I am trying to use the pull code to constrain the distance between the center
mass of two molecules but I am obtaining very high oscillations (between 1000
and -1000) in the
output.pdo. I need those forces since the idea is to run different simulations
with the molecules at different distances and then integrate to calculate the
work along this path. Something similar to pull out A from B but avoiding the
dynamic effects. I am currently using gromacs 3.2 and my pull.ppa file is as

 runtype = constraint
 group_1 = A
 reference_group = B
 reftype = com
 pulldim = Y Y Y
 constraint_direction = 1.0 1.0 1.0

I am using constrain_rate = 0 and constrain_tolerance = 1E-6 (the default
values) and I guess that there would be my error but I do not know which values
would be suitable since I do not know exactly how the algorithm works. Anybody
can help me?

A second question: Doesn't the pull code work in parallel? From the mailing list
it seems that it does not in previous versions but I do not know in 3.2

Thanks for any help!

Angel Pineiro.

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