yes that reference for Amber18 is fine - my point is that there is no
specific program called Amber, so that reference works for sander and
should be ok. You can assure your committee member that Amber and Sander
are not different things - sander is one part of Amber.
On Mon, Apr 13, 2020 at 1:18 PM Erdem Yeler <erdemyeler.gmail.com> wrote:
> Hi, thanks for your answer. Yes I saw the same page. Actually I shortened
> my reference. I used the first reference in the page ( "When citing
> Amber18 or AmberTools18 please use the following:" section ) But you are
> saying I am wrong. I understood from that I should use "An overview of the
> Amber biomolecular simulation package" article and "The Amber
> biomolecular simulation programs." article both for reference. Because
> rest of them are force field and gpu accelerated articles.Did I understood
> correctly?
> Thank you again,
> Erdem
>
>
>
> Carlos Simmerling <carlos.simmerling.gmail.com>, 13 Nis 2020 Pzt, 19:19
> tarihinde şunu yazdı:
>
> > 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:
> >
> > https://ambermd.org/CiteAmber.php
> >
> > On Mon, Apr 13, 2020 at 12:13 PM Erdem Yeler <erdemyeler.gmail.com>
> 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 :
> > > https://ambermd.org/CiteAmber.php
> > > 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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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Apr 13 2020 - 10:30:03 PDT
