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
The Scripps Research Institute
10550 North Torrey Pines Road, TPC-15
La Jolla, CA 92037
TEL: (858)784-9788
FAX: (858)784-8896
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
>
> --
> Marios Philippopoulos, PhD
> Structural Biology and Biochemistry Programme
> Hospital for Sick Children
> 555 University Avenue
> Toronto Ontario Canada M5G 1X8
>
> mphilip_at_sickkids.on.ca
>
>
>
Received on Mon Mar 06 2000 - 13:12:25 PST
