Hi,
I am trying to calculate the PMF of two peptides using constraint in gromacs
4.0.5. But, I am finding a very large oscillation( from -1000 to +1000) in the
force that is being printed in pullf.xvg file . Is this oscillation normal ? In
that case at any distance, the mean force will be zero ( I assume).
Here is the excerpt of the mdp file:
; pull code
pull = constraint
pull_geometry = distance
pull_dim = Y Y Y
pull_init1 = 1.5
pull_k1 =
pull_group0 = CA1
pull_ngroups = 1
pull_group1 = CA2
pull_nstxout = 50 ;step
pull_nstfout = 20
Thanks
Jagannath
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