[AMBER] Reaction Coordinate that is the Difference of two Distances

From: <diego.soler.uam.es>
Date: Wed, 14 Mar 2018 16:24:01 +0100

  Dear all,

I want to perform Umbrella Sampling simulations and Steered Molecular
Dynamics with a reaction coordinate that is a combination of two
distances, d1 & d2. d1 is the distance form one atom to another, and
d2 is another distance between another pair of atoms, and the reaction
coordinate that I want to use is d2-d2. Is this possible? How can I
achieve this?

The restriction files I am using look like

&rst iat=6,6,
       iresid=1, ifvari=1,nstep1=0, nstep2=1000,
       atnam(1)='N1', atnam(2)='H1'
       r1=0.000, r2=0.9000, r3=1.1000, r4=10,
       r1a=0.000, r2a=0.900, r3a=0.900, r4a=10,
       rk2=500, rk3=500,rk2a=2000, rk3a=2000,

Here there is just one distance (from the atom N1 to the atom H1). I
know I can add as many restrictions of this sort as I want, but I want
a single restriction (that is, a single harmonic/umbrella potential)
over a single coordinate that is d2-d1.

Thank you for your help!

Diego SP

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Received on Wed Mar 14 2018 - 08:30:03 PDT
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