From: David A. Case <>
Date: Thu, 2 Mar 2006 12:42:39 -0800

On Thu, Mar 02, 2006, wrote:

> I carried out two simulations on the same RNA molecule using both AMBER 8
> and AMBER 7.

> Surprisengly the minimized structures look very diffent

This is surprising, since a few thousand steps of energy minimization rarely
changes the structure very much. Presumably(?) there could be no differences
in the restrained minimization [unless you in fact had different starting
structures....]. Even an unrestrained minimization for such a short time
should not do much -- *unless* you have some very bad forces and energies
in the starting structures.

> and the
> unrestrined MD trajectories show a very different behaviour:

This is to be expected, given what you said: if the minimized structures
(which are what you used to start the MD) are very different, then the
MD simulations themselves are likely to be different.

You don't give much information, but I would look at the minimization step
to see if you can figure out what is going on there.

[All of this should have nothing to do with Amber 7 vs. Amber 8. To test
this, run a short MD or minimization (just a few steps), set ntpr=1, and
compare the results with both programs.]


> Keep RNA fixed with weak restraints
> 10.0
> RES 1 24

Just a comment on the above: restraints with a force constant of 10 are in
fact very strong restraints; a "weak" restraint would be something like 100
times smaller than that.

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Received on Sun Mar 05 2006 - 06:10:17 PST
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