Dear Sir/Madam,
I could like to ask if AMBER include the 0.5 when they specify
spring constants for their restraint terms?
If examples, if we assume the biasing potential used for PMF
calculations is of the format (required for WHAM calculations):
V = 0.5 k (x - xo)^2
And did the restrainst as it is listed below
# variable distance restrainst
&rst iat=4,5 r1=0.0, r2=20.0, r3=20.0, r4=100.0, rk2 = 100.0, rk3 =
100., iresid=1,
ATNAM(1)=P,
ATNAM(2)=O18/
Is the spring constants equal to 100?
Best regards,
Cat
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Received on Sun Jun 17 2007 - 06:07:18 PDT
