AMBER Archive (2007)

Subject: Re: AMBER: Harmonic constraints

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Sep 07 2007 - 10:31:46 CDT

the value entered in the input is indeed k/2 for positional restraints.
look in ene.f at the xconst() routine.

you should almost certainly not be using ff99, it is well documented that
it has very bad properties.

On 9/7/07, Johan Qvist <johan.qvist_at_gmail.com> wrote:
>
> Dear Amber community,
> I am using Sander (under Amber 8) and the ff99 forcefield to run MD
> simulations with cartesian hamronic restraints on some atoms, (i.e. using
> NTR = 1). Now my question is simply if the specified force constant enters
> as k/2*(x - x0)^2, as commonly definied, or as k*(x-x0)^2? The question
> might be stupid but while I was reading the manual I got the impression that
> the latter could be the case as all forcefield references in the manual are
> to this form.
>
> It would be great if someone could dispell my doubts.
>
> Best regards /Johan Qvist
>

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