[gmx-users] Steered MD in reverse direction?

Sanku M msanku65 at yahoo.com
Fri Nov 4 02:24:57 CET 2011

  I am performing steered Molecular dynamics simulation to pull a molecule out of a complex. I am using gromacs 4.5.4 to perform the constant rate pulling..I have done the steered MD simulation in a particular direction i.e hav pulled the molecule out of complex.
But, to check the convergence/hysterisis of the pulled path way, I would like to perform the same steered MD in reverse direction i.e push the molecule back into the complex. But, I was wondering, to perform the backward steered MD, how should I modify the .mdp parameters?  Should I make the pull_rate1 negative or switch the pull_group0 and pull_group1 ?  Any help will be appreciated.

The following is the part of the pull-code parameter I am using:
; Pull code
pull            = umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim        = N N Y
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = Mol_A
pull_group1     = Mol_B
pull_rate1      = 0.0025      ; 0.01 nm per ps = 10 nm per ns
pull_k1         = 1000      ; kJ mol^-1 nm^-2

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