AMBER Archive (2007)

Subject: Re: AMBER: (no subject)

From: Franck Vendeix (Franck_Vendeix_at_ncsu.edu)
Date: Thu Jun 14 2007 - 08:32:54 CDT

The force constant that needs to be used with WHAM is 200
kcal/(mol.A^2) since V = k (x - xo)^2 in Amber.
Franck

Catein Catherine wrote:
> 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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