AMBER Archive (2005)

Subject: RE: AMBER: Add constraints over time

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Aug 26 2005 - 11:41:04 CDT

Dear Andrew,

> Is there a way to increase the constraint force linearly from
> 0 to 30 kcal
> mol-1 Å-2 over time?
> The MD run length is1002.5 ps, in which the linear increase
> of the distance
> constraints will only be over the first 2.5ps (following a
> protocol set up
> in J. Mol. Biol. (1999) 290, 699-716 by M.S.Searle et al.)

I assume you mean to vary the restraints rather than constraints. I believe
you can do this using the weight change function coupled with NMR
restraints. This is fairly involved since I don't believe you can actually
vary the value of restraint_wt that is used for harmonic restraints. Instead
you would have to set up a series of NMR restraints. It should be possible
though to construct the same restraints.

An alternative if you only want to do this a few times, would be to modify
the code. If you take a look at the subroutine xconst (ene.f), called from
force (force.f) you will find where the position restraints are calculated.
The restraint_wt is passed in as an array called xc which should contain one
entry for each atom. You could quite easily add an extra argument to force
and then to the call to xconst that contains the value of nstep. Then inside
xconst you could calculate a scaling factor (0.0 to 1.0) for restraint_wt
based on the value of nstep with relation to the window where you want to
scale the restraints. Then whenever xc is used inside xconst just multiply
it by this scaling factor.

I hope this helps
All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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