Re: [AMBER] SHAKE ALgorithm and frcmod file

From: David A Case <>
Date: Fri, 1 May 2020 08:34:04 -0400

On Fri, May 01, 2020, Elif Çiğdem Calvin wrote:
>Actually in the manuscript, I just mendtioned I used SHAKE Algorithm and I
>didn't say in the manuscript "... we used SHAKE in order to apply bond

Note that with the common setting of ntc=2, Amber shakes only bonds to
hydrogens, so only those energies will go to zero. So, you will still
have bond energies for bonds between heavy atoms.


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Received on Fri May 01 2020 - 06:00:03 PDT
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