research at khinsen.fastmail.net
Mon Aug 26 18:27:17 UTC 2013
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From: mmtk-bounces at starship.python.net
To: mmtk-owner at starship.python.net
Subject: Auto-discard notification
Date: Mon, 26 Aug 2013 15:21:11 +0000
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From: Edvin Fuglebakk <edvin.fuglebakk at gmail.com>
To: "子茗" <810918909 at qq.com>
Cc: "mmtk" <mmtk at starship.python.net>
Subject: Re: [MMTK] about the spring constant
Date: Mon, 26 Aug 2013 12:01:44 +0200
I will offer a few thoughts on this one.
It is very difficult to find a reliable source of thermal fluctuation to use as a
standard for parameterizing the spring constants in any elastic network model. If
you could describe the downstream analysis you want to do of the model, maybe the
MMTK-lists can provide suggestions. Most kinds of analysis that are commonly done
with elastic network models are formulated in ways that only requires this
parameter to be decided up to a global constant (which means that any value will do
for a network with uniform spring constants).
Although there is some conflicting use of three letter abbreviations for elastic
network models, the GNM is usually taken to be the Gaussian Network Model (I.
Bahar, A. R. Atilgan, and B. Erman, “Direct evaluation of thermal fluctuations in
proteins using a single-parameter harmonic potential,” Folding Des., vol. 2, no. 3,
pp. 173–181, Jun. 1997.) You should be aware that the interaction potential
underlying this model, and the physical interpretation that can be made of it, is
different from any of the elastic network models implemented in MMTK.
On 26. aug. 2013, at 11:05, 子茗 wrote:
when use the GNM to calculate the dynamics of a protein, there is a variable to
be set,the spring constant.
However, I have no idea about it, how to set it? some papers have referred to
the least square fitting? how is the procedure?
and when use the least square fitting, whether to take the K_B*T/gama as an
integral or not? and the value of temperature,T,how to find it?
mmtk maillist - mmtk at starship.python.net
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