Date: Mon, 6 Mar 2000 13:12:25 -0800 (PST)
From: Vickie Tsui
Subject: Re: Harmonic restraints on distances in sander

You could use distance restraints provided as part of the NMR refinement
utilities to impose harmonic restraints on inter-atomic distances. Right
now the penalty function is such that you can enter r1, r2, r3, r4 values.
If R is the current distance, then the penalty function is:

R < r1 linear
r1 <= R < r2 parabolic
r2 <= R < r3 Epenalty = 0
r3 <= R < r4 parabolic
r4 <= R linear

If you want a purely harmonic function, set r1 to 0, r2=r3, and r4 to a
large number, and that should work.

vickie


On Mon, 6 Mar 2000, Marios Philippopoulos wrote:

> Is it possible to impose harmonic restraints on inter-atomic distances
> during an MD run using sander? Would I have to use the NMR utilities for
> that purpose (section 4 of the sander manual)? I want to perform an
> umbrella sampling calculation.
>
> Thank you for any replies,
>
> Marios Philippopoulos
>