Hi,
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
Sanku
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