AMBER Archive (2008)

Subject: Re: AMBER: NAB parameter: wcons

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Sep 10 2008 - 07:19:32 CDT

On Mon, Sep 08, 2008, ramu_at_vt.edu wrote:
>
> Do you know if the units for the Restraint Weight, wcons, in NAB is the same
> as the RESTRAINT_WT in Sander (kcal/mol-A^2)? What are typical values for
> minimization and equilibration?

I believe these are equivalent, but you can test yourself, by running a
simple minimzation (or single point calculation) in both sander and nab.

Values don't generally need to be very large to keep structures from
moving much from their initial positions. While the actual values
depend on the structure and how good or bad the intial coordinates are,
I often use something like 5 kcal/mol-A2 for minimization and initial
MD equilibration, then reduce this to 1, and then to 0.1, for subsequent
equilibrations. Then, I do some final equilibraiton with no positional
restraints. But that is just a general guideline: you should always
study (but visually and by examining the energy outputs) the behavior of
*your* system.

...dac

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