Dear Pooja,
The AMD code in AMBER 12 has been extensively tested and heavily
optimized, including support for running on GPUs:
Pierce, L.C.T., Salomon-Ferrer, R. de Oliveira, C.A.F. McCammon, J.A.
Walker, R.C., "Routine access to millisecond timescale events with
accelerated molecular dynamics.", Journal of Chemical Theory and
Computation, 2012, 8 (9), pp 2997-3002, DOI:10.1021/ct300284c
<
http://dx.doi.org/10.1021/ct300284c>
I would highly suggest upgrading to AMBER 12 and using that rather than
wasting time trying to implement it in Amber 9 (which is roughly a 6 month
job). Details for obtaining Amber 12 are here:
http://ambermd.org/#obtain
If your research group do not have the funds to purchase AMBER 12 then you
can request a waiver of the AMBER 12 fee as noted in those instructions.
All the best
Ross
On 1/15/13 3:18 AM, "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.
>> > > > _______________________________________________
>> > > > AMBER mailing list
>> > > > 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
>> > > _______________________________________________
>> > > 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
>>
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Received on Tue Jan 15 2013 - 08:00:06 PST
