[AMBER] Berendsen vs. Monte Carlo

From: Parker de Waal <Parker.deWaal.vai.org>
Date: Fri, 25 Jul 2014 02:14:06 +0000

Hi Everyone,

I haven't been able to find any literature, besides the manual, describing the implementation of the Monte Carlo barostat in AMBER14 and was wondering if someone could provide some insight.

Currently I'm trying to sample the energy landscape of an apo protein using aMD that I suspect is very unstable, due to the geometry of the ligand binding pocket, and suspect will undergo a large significant change. Because of this I would like to use the NPT ensemble during my production MD instead of NVT to allow a greater range in energy fluctuation. If possible I would like to use ntb =2, ntp =1, barostat = 2 to save computer time and speed along the process, however I'm concerned that the Monte Carlo barostat won't be as effective as the Berendsen implementation to achieve this goal.

Any input on this topic would be appreciated.

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Received on Thu Jul 24 2014 - 19:30:02 PDT
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