On Mon, Jun 29, 2015 at 8:02 AM, Yogeeshwar Ajjugal <
bo14resch11004.iith.ac.in> wrote:
> Dear Amber community,
>
> I have larger system with size of
> 3,20,000 atoms which requires higher running time scale in Amber suite.
>
I'm assuming this means 3,200,000 atoms (3.2 M). Otherwise, Amber
programs are quite well-equipped to handle 320,000 atoms.
>
> Therefore, I would like to know if Amber force field could be used in NAMD
>
> and if so, how reliable is that?
>
See
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node13.html for
instructions *from* NAMD for this and
http://ambermd.org/namd/namd_amber.html for instructions *from* Amber for
this.
It's also possible that GPUs with a lot of memory can still handle 3.2 M
atoms, so if you have a 6 GB (or more) GPU, it may be worth just trying it
if you have access to pmemd.cuda.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 29 2015 - 05:30:05 PDT
