[gmx-users] [Fwd: a question about your reply]

Mark Abraham mark.abraham at anu.edu.au
Wed Jul 4 10:56:10 CEST 2007

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.


---------------------------- Original Message ----------------------------
Subject: a question about your reply
From:    ÀïÃÎ <limeng9505 at tom.com>
Date:    Wed, July 4, 2007 6:37 pm
To:      mark.abraham at anu.edu.au

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

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