Metadynamics Colvar UNITS and how to define COM

cjor chri... at gmail.com
Mon Jan 30 12:46:06 CET 2017


Hello,  I'm using Plumed2 for my metadynamics calculation.

I have a diatomic gas molecule exploring distance between H2 and metal
center. 

Initially I used a simple Distance colvar (between one gas atom and metal), 
but it gave me 2 minima probably
because the gas atom can flip. So I want to use center-of-mass (COM) of gas 
molecule and the metal.

My question:

(1) I can't seem to find a simple way of doing this [why is there no option 
for groups in the Distance colvar?]

I tried this but it's not elegant.

 &COLVAR

 &DISTANCE_FUNCTION

 ATOMS 4276 4277 3775 3775

 COEFFICIENT -1.00000

 #  distance 1 = ( 4276 - 4277 )

 #  distance 2 = ( 3775 - 3775 )

 &END DISTANCE_FUNCTION

 &END COLVAR


(2) What is the unit of the Distance colvar? 
I want it to be Angstrom. I am specifying Angstrom for the ABC of the box, 
does this translate
to the same unit ? 

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