AMBER Archive (2004)

Subject: RE: AMBER: Minimization error

From: Ross Walker (
Date: Sat Aug 28 2004 - 14:34:31 CDT

Hi Armin,

> As over the first 100 steps the values were exactly the same,
> when coming
> from the same input structure, the installations seem to be ok and the
> problem (although it isn't really one, as the MD seems to
> work) is just
> that my structure has a hard time converging on a minimum
> energy during
> minimization. Is this correct, or did I misunderstand something?

No, that's exactly what I meant. All you MD is the same so you are probably
ok. You just have some instability in your minimisation of your structure.
Possibly the potential energy surface is very flat around the starting
structure so rounding errors can cause it to go off in different directions.
I would thus trust your starting structure and run some long MD now and see
if your system is stable. It may not be due to the trouble minimising it but
you won't know until you run quite a bit of MD.

Good luck.

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to