AMBER Archive (2004)

Subject: RE: AMBER: RMS of energy in Minimization using SANDER

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Nov 17 2004 - 12:36:25 CST

Dear Jack,

You don't say how big your system is. If it is a big system then you will
need many more than 1000 steps to reach a good minimum. Typically you will
need to do more steps than you have degrees of freedom. So 1000 atoms = 3000
degrees of freedom so you need 5,000 or more steps.

> Sander input file:
> ___________________________________________________________
> &cntrl
> imin=1, maxcyc=1000, cut=8.5, ntb=2, ntp=1, igb=0,
> &end
> ___________________________________________________________
>
> The RMS is around 0.44.
>
> 1. Is it normal? In other minimization jobs, I even got 2.47 RMS.

Try doing 2000 steps of steepest descent followed by 20,000 steps of
conjugate gradient. If you set DRMS then the minimisation will stop when the
rms is below this.

E.g. for 1x10-5 try:

ncyc=2000,maxcyc=22000,drms=0.00001,

If it still hasn't finished minimising after 22000 steps try a few more...

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

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