Hi All,
In general what we do in pulling simulations that we pull one
selection keeping the other fixed. In that case the distance between the two
selections increases with time. Now, I want to push the selections i.e. one
selection will be kept fixed and the other will be pushed towards the fixed one
so that the distance between the two selection will decrease. Is it possible to
do that in GROMACS? What should I modify in the mdp file? I am attaching a mdp
file that I have used for pulling simulations (only the pull part).
; pull code
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = freeze
pull_group1 = pull
pull_rate1 = 0.01
pull_k1 = 1000
I have used pull_dim N N Y as I am interested to pull only in the z direction.
Should I just use N N -Y to do the compressing simulations?
Please suggest.
Thanks in advance.
Samrat
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