AMBER Archive (2006)Subject: Re: AMBER: dihedral angle equation
From: Igor Schapiro (igor.schapiro_at_uniduisburgessen.de)
Date: Fri Nov 17 2006  08:15:47 CST
Hi Vitor,
you will find the answer on the next page (p.258) in the same manual, if you
read it carefully: "PK is equal to onehalf of the barrier magnitude" which
is equal to Vj/2. And the value of IDIVF depends on the substituents of the
bond which rotates. "If all atoms are explicit, then IDIVF=1 ...".
The first equation that you mentioned (p.257) is a general description of the
torsional potential energy function, whereas the second (p.89) is a special
case where IDIVF=1. For this special case the equations are equal.
Best regards,
Igor
Am Freitag, 17. November 2006 13:41 schrieb Vitor Manuel Sousa F?x:
> Dear Amber users
>
> anyone can tell me which is the relationship between in
> the ETirs formula PK/IFDIV (pag . 257 amber 8 manual) and
> the VJ/2 in dihedral equation used by sander (pag 89). The
> two terms are equal ?..
>
> Thanks a lot in advance
> Vitor
>
> *****************************
> Vitor Felix
> Department of Chemistry
> University of Aveiro
> 3810193 Aveiro
> Portugal
> Tel: 351 234 370 729
> 
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==============================================================
Igor Schapiro
Universität DuisburgEssen
Theoretische Chemie
email igor.schapiro_at_unidue.de

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