Re: [AMBER] integration algorithm of sander? And reference of sander?

From: Carlos Simmerling <>
Date: Mon, 13 Apr 2020 12:18:54 -0400

sander is one of the programs in the Amber package. There is no individual
program in the package that is called Amber. Technically it is part of
Amber Tools, but the is not really relevant for the citation that you need.
See the Amber web page:

On Mon, Apr 13, 2020 at 12:13 PM Erdem Yeler <> wrote:

> Hi,
> I completed my thesis and I used sander program for minimization, heating
> and md simulation. Today, one of jury member asked me via e-mail:
> 1) What is the integration algorithm is it velocity, Verlet or leap-frog?
> *Actually I used SHAKE algorithm and according to my knowledge the SHAKE
> is a verlet algorithm (amber uses velocity-verlet algorithm and it conserve
> energy well in NVE simulations). but I am not sure. Am I wrong?
> 2) For sander program I referred to AMBER from here :
> My Reference was
> "D.A. Case, et. al , AMBER 2018, University of California, 923s. San
> Francisco.
> but the jury asked me to show another reference for only sander program.
> They think amber and sander are different things. Actually I knew sander
> and/or pmemd is amber itself :) But after jury's question I am not sure
> anymore. Should I use another reference for sander?
> Thank you
> Erdem
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Received on Mon Apr 13 2020 - 09:30:02 PDT
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