AMBER Archive (2004)

Subject: Re: AMBER: torsion scan

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Tue Jul 13 2004 - 16:12:50 CDT

Hi, Dave

The force constants seem large, but they are meant for torsion angles.
The unit of force constant for torsion angles is kcal/(mol*rad^2). 5000
is about 1.52 kcal/(mol*degree^2). I found the input worked fine after I
changed nstlim and nstep2 to 3600 (I actually had to calculate the
torsion angles of the snapshots to see the rotation). So I guess I
misintepreted the restraint energy in the mdout.

Regards,

Guanglei

David A. Case wrote:

> On Tue, Jul 13, 2004, Guanglei Cui wrote:
>
>
>> rk2 = 5000, rk3 = 5000, rk2a = 5000, rk3a = 5000,
>
>
> These are incredibly strong penalties; try reducing them by 2-3 orders of
> magnitude. (Not sure that this is the only problem, but this certainly
> needs attention.)
>
> ...dac
>
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