Dear Amber experts,
I was trying to conduct steered MD to pull two domains of a protein in
opposite directions with a constant force using Amber 20. I was trying
to apply the constant force along x-axis on the centres of masses of the
two protein domains.
As I understand, there are two methods to conduct steered MD simulations
in Amber - with Jarzynski Relationship (input keyword - ‘jar’), and with
reaction coordinate approach (input keyword - ‘infe’ with &smd
namelist).
For the approach with Jarzynski Relationship, I understood that the
force is calculated from the relation F = - 2 * rk2 * (x-x0(t)). To
apply constant force along x direction on the centres of masses (with
‘fxyz=1,0,0’ and ‘igr’ within &rst) I had set the values of r1 to r4
to a value much larger than the initial distance between the centres of
masses along x, such that, it is in the linear region of the potential
and hence expecting that a constant force would be applied (following
the suggestion in
http://archive.ambermd.org/201104/0662.html). But from
the four column output (x0(t), x, force, work) I see that x0(t), and
hence the force changes along the pulling. How is x0(t) calculated in
each step of steered MD with ‘jar’ approach?
For the reaction coordinate approach, I understood that collective
variable type ‘COM_DISTANCE’ would increase the overall distance between
the centres of masses, and not in a particular direction. Is there a way
by which constant force could be applied in a particular direction (say
x-axis) on the two centres of masses using the reaction coordinate
approach?
Thanking you,
Prithvi
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Received on Tue Aug 03 2021 - 13:00:02 PDT
