AMBER: SHAKE in thermodynamic integration

From: by way of riccardo nifosi <riccardo>
Date: Thu, 20 May 2004 12:38:21 +0200

Dear all,

I'm trying a free energy calculation of a threonine to serine substitution
with the thermodynamic integration module of sander (I'm using amber7).
What is the behavior of shake when the equilibrium distance between the dummy
hydrogens (those of the disappearing methyl) and the carbon is different in
the perturbed and unperturbed systems? I noticed that though shake is turned
on these distances vary during the MD window run, so I suppose that they are
not constrained. Using shake in my case would not be correct... Am I right?

Thank you,
Riccardo Nifosi
Nest-INFM, Scuola Normale Superiore
Piazza dei Cavalieri n.7
I-56126 Pisa
web page

Tel: +39-50-509412
Fax +39-50-563513

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Received on Thu May 20 2004 - 11:53:00 PDT
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