[AMBER] Constant external force in the given space zone ? Thermostat working just on selected part of simulated system ?

From: Marek Maly <marek.maly.ujep.cz>
Date: Fri, 11 Jan 2019 15:38:54 +0100


I would like to know, if it is possible in Amber 18 (in ideal case in
"pmemd.cuda" simulation )

1) In the given part of the simulation box apply to selected (or
eventually to all) atoms constant
external force. I.e. if the atoms are in the given zone of the simulation
box, a constant external force acts on them if they are outside this zone,
the force stops acting.

2) In NVT simulation to apply thermostat just to some part of the
molecular system (i.e. to atoms defined by mask).

I am asking in the context of calculation of gas permeabilities using
Non-Equilibrium Molecular Dynamics
see for example figure 4 here:


Whole article available here:


      Thanks in advance for information.

                  Best wishes,


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Received on Fri Jan 11 2019 - 07:00:02 PST
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