AMBER Archive (2009)

Subject: [AMBER] Actual force constant in SMD

From: Dmitri Nilov (nilovdm_at_gmail.com)
Date: Mon Mar 16 2009 - 13:07:09 CDT

Hello, I wander what actual force constant is used in SMD method in case of
distance restraint (Amber 10).
What rk2 value should I define if I want to use constant k=10 kcal/mol*A2
for equation V=1/2k[(x-x0)**2]? 5 or 10?
This question is related to my observation of force value in SMD output file
that is twice than expected from formula f=rk2*(x-x0),
and to information found in mailing list:
"The force constant will be twice the values you give for rk2=rk3 because
Amber historically does not include a factor of 1/2 in constraint
energies".
Coud you help please?!

Dmitri Nilov,
Lomonosov Moscow State University
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