Re: AMBER: reporting atoms clashed during simple energy minimization

From: Dr. Yong Duan <>
Date: Tue, 9 Sep 2003 08:18:44 -0400 (EDT)

The simple answer is no. There is presently no mechanisms in sander to
report that. I thought leap does report it when it occurs. To do it in
sander, we need to add an IF-THEN-ENDIF block within the inner loop of the
non-bonded force calculation. This is not desirable since it may slows
down the performance quite a bit.

Atom classes can due to two types of close contacts.
1) Two atoms are initially too close to one another and they are
in a "crowded" environment. In this case, it is relatively difficult to
deal with. But I suspect a combination of small steps and the SHAKE should
make it easier.
2) Atoms that are initially separated somehow get together too close.
This happens mostly in the cases when one of the atoms' van der Waals
radius is zero (e.g., H of TIP3P water). And, this is also related to a
somewhat large step in energy minimization. The energy barrier separating
the two atoms is small and narrow. A reasonable fix is that a) run a
100-step minimization with SHAKE on and with a small minimization limit.
The later should always be used anyway.


On Tue, 9 Sep 2003 wrote:

> Hello,
> I use sander for simple energy minimization (without molecular dynamic
> simulation).
> Is there any method that can report the atoms clashed during the
> minimization?
> For example, if the distance of the non-bonded atoms is less than 1.5
> A, it can report the warning.
> Thanks.
> Jackie Chen
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Received on Tue Sep 09 2003 - 13:53:01 PDT
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