Thank you soo much :)
Carlos Simmerling <carlos.simmerling.gmail.com>, 13 Nis 2020 Pzt, 20:27
tarihinde şunu yazdı:
> 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
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 13 2020 - 11:00:01 PDT
