RE: minimization probs

From: case <>
Date: Tue 11 Jun 2002 10:36:57 -0700

>===== Original Message From "Amesh Patel" <> =====

>i have a system consisting of a protein with a carbohydrate ligand. when
>i try to minimize it using the following input file, the end structure
>isn't actually a minimium energy strucutre. so when i try to minimize it
>further by another 500K steps, the energy and rms do indeed decrease but
>then halfway through they increase and don't stop increasing (not quite
>the point of minimization methinks). i have set the cut to 999ang and
>the nsnb to 99999999 but the electrostatic energy figure goes off the
>scale and the thing never minimizes.
> &cntrl
> imin=1,
> maxcyc=100000,
> ntpr=200,
> cut=8,
> nsnb=999999,
> ntmin=2,
> scee=1.2,
> ntb=0,
> &end

I think you should try a much more conservative strategy. Try minimizing for
100 steps (not 100000), print every step, set ncyc=100 (to get just steepest
descents). Try to see that everything is working OK (esp. with a large

Then you can slowly try to turn on conjugate gradient minimization. There is
generally no need to do more than a few hundred steps of minimization if the
purpose is to prepare the system for later MD, but you will want to follow
things quite carefully if you energies are funny -- look at the coordinates
before and after big increases in electrostatics to see what might be going

To say more, one would need to have a lot more information.

...good luck...dac

David A. Case | e-mail:
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA |
Received on Tue Jun 11 2002 - 10:36:57 PDT
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