AMBER Archive (2007)

Subject: Re: AMBER: regarding distance restraints

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Jul 23 2007 - 06:26:27 CDT

did you read page 180 of the Amber9 manual?
all of the "a" values are the final values if you change
the restraint during the run (if you set ifvari=1).
otherwise the a values aren't needed.
rk2 and rk3 are the force constants for each side of the parabola.
no energy between r2 and r3, and between r1 and r2 it is
a parabola with force constant rk2. between r3 and r4 it
is a parabola with force constant rk3. outside r1 or r4 it
is linear, usually only useful if your initial structure does not
satisfy the restraints and you don't want huge forces that
a parabola would give.

On 7/23/07, gurpreet singh <gps.iitm_at_gmail.com> wrote:
> Hello users
>
> I have to use some distance retraints between two atoms in a simulation. I
> am using this distance restraint for the first time. i read the manual but
> no clear definition of r1,r2,r3,r4 rrk2a,rk3 is given in it.
>
> i would be glad if some one can tell me the meaning of each of these or
> just tell the source form where i can read about this
>
>
> thanks
> with regards
> Gurpreet
>
>
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