The paper may help with implementing AMD in AMBER 9. I would plan to
spend a semester or three doing it. Spending a day to a week studying
the code will get you started.
Bill
pooja chahal <chahal.pooja.rs.gmail.com> wrote:
> Dear Bill,
> I just want to ask about modification that can be done in AMBER 9 suite to
> implement AMD in it? There is a paper in McCammon's paper in JCP in 2004 in
> which they have done some modification in AMBER 7 so that AMD can be
> performed in that suit. My interest is to have some idea about those
> modifications.
>
> On Sat, Jan 12, 2013 at 10:31 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > If you have the physics and the math and the programming skills, then
> > all you need is to understand the existing code. If you study that for
> > a day you should start to get the lay of the land.
> >
> > Bill
> >
> > pooja chahal <chahal.pooja.rs.gmail.com> wrote:
> >
> > > I don't have AMBER 12 with me and i think right now it won't be possible
> > to
> > > install AMBER 12. I can implement in AMBER 9 itself but i am not sure how
> > > to do it. Can you please suggest way to implement it in AMBER 9.
> > >
> > > On Fri, Jan 11, 2013 at 6:57 PM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> > >
> > > > Amber 12 has AMD capabilities in sander, pmemd, and pmemd.cuda. Unless
> > > > you're ready to implement AMD on your own inside Amber 9, you should
> > > > upgrade to Amber 12.
> > > >
> > > > HTH,
> > > > Jason
> > > >
> > > > On Fri, Jan 11, 2013 at 5:28 AM, pooja chahal <
> > chahal.pooja.rs.gmail.com
> > > > >wrote:
> > > >
> > > > > Dear,
> > > > > I want to simulate a protein using Accelerated Molecular Dynamics
> > and I
> > > > > have AMBER 9 installed in my machine. In short I want to do it on
> > AMBER.
> > > > > Can anyone suggest me how to do it? or Is there any way to perform
> > this
> > > > in
> > > > > any version of AMBER?
> > > > > Thanks in advance.
> > > > > _______________________________________________
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> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Jason M. Swails
> > > > Quantum Theory Project,
> > > > University of Florida
> > > > Ph.D. Candidate
> > > > 352-392-4032
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> > > >
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Received on Tue Jan 15 2013 - 15:30:03 PST
