[gmx-users] large oscillation in mean force with constraint

Sanku M msanku65 at yahoo.com
Sat Apr 24 07:45:37 CEST 2010

  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


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