Re: [AMBER] Running amber forcefield in NAMD

From: Jason Swails <>
Date: Mon, 29 Jun 2015 08:12:52 -0400

On Mon, Jun 29, 2015 at 8:02 AM, Yogeeshwar Ajjugal <> 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 for
instructions *from* NAMD for this and for instructions *from* Amber for

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.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 29 2015 - 05:30:05 PDT
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