AMBER Archive (2004)

Subject: AMBER: SHAKE in thermodynamic integration

From: by way of riccardo nifosi (r.nifosi_at_nest.sns.it)
Date: Thu May 20 2004 - 05:38:21 CDT

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
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