On 7/4/2007 4:56 PM, Mark Abraham wrote:
Please keep conversations on the list in case others want to contribute,
and so the outcomes are stored for others to search for.
I thought I answered your current question when I observed that the
deviations you observe seem normal. The size of these deviations will
depend on the nature of your system and how much thermal energy is going
around. Nobody is likely to think anything of a few degrees. The molecular
mechanics approximation isn't going to reproduce geometries to closer than
that sort of difference anyway.
You may use all-bonds (bonds and angles) for constrains to reduce
high-frequency motion for bonds, but for torsional, your result is alright.
The inter-atomic interaction in force fields are merely model, which
doesn't necessarily to bear physical meaning. Bond and angle in force
fields may find their counter-parts in quantum mechanics but they are
still different. Torsional is primarily to correct the remaining energy
or to constrain certain structure. Having small fluctuation means that
such correction is working well.
Mark
---------------------------- Original Message ----------------------------
Subject: a question about your reply
From: ÀïÃÎ <[EMAIL PROTECTED]>
Date: Wed, July 4, 2007 6:37 pm
To: [EMAIL PROTECTED]
--------------------------------------------------------------------------
Dear Mr Mark,
Thanks very much for your reply, but I think I did not describe my
question clearly in my last letter.
I know the value will move around the minimum defined at 120 degrees when
using harmonic potential and the dihedral will deviate from 120 degrees
during the simulation, but I don't know what magnitude of deviation is
proper for the simulation. For example, in my simulation, the maximum
deviation is 2 degree, is it too big or proper? Or should I
control the maximum deviation as small as possible?
Meng Li
2007.7.4
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Dear Mr Mark,
Thanks very much for your reply, but I think I did not describe my
question clearly in my last letter.
I know the value will move around the minimum defined at 120 degrees
when using harmonic potential and the dihedral will deviate from 120
degrees during the simulation, but I don't know what magnitude of
deviation is proper for the simulation. For example, in my simulation,
the maximum deviation is 2 degree, is it too big or proper? Or should I
control the maximum deviation as small as possible?
Meng Li
2007.7.4
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