[AMBER] Clarification of Amber Post on Heating Protocol

From: Robert Molt <rwmolt07.gmail.com>
Date: Tue, 14 Jul 2020 17:46:25 -0400

Good evening,

I wanted to clarify a particular post from the esteemed Ross Walker from


I noticed that Dr. Walker wrote wrote:

"It is critical to initial heat using NVT because at low temperatures the
calculation of pressure is inaccurate and can cause the barostat to
overcorrect leading to instabilities. I typically either heat to 100K or so
and then switch to NPT or I run a short (20ps or so) heating stage. The key
is not to run for too long initially in NVT (before NPT) or you will get
vacuum bubbles form in the solvent."

My confusion is: does one not have a "discontinuity" of sorts in heating
to 100K and then immediately beginning the NPT equilibration at T=300?
Is the effect perhaps "small," such that it is irrelevant?
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Received on Tue Jul 14 2020 - 15:00:03 PDT
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