Re: [AMBER] Metadynamics in pmemd

From: David A Case <>
Date: Mon, 29 Jan 2018 12:01:42 -0500

On Thu, Jan 25, 2018, Hannes Konegger wrote:
> Since I slowly want to extend my reportoire of applicable MD methods, I
> wanted to ask you if any official implementation of the PLUMED software
> to pmemd will be available in the (near) future? Up to now, this
> functionality is only available in the sander module, thus the
> advantages of MetaD cannot be fully utilized due to restrictions in
> sampling speed. I guess this topic might not be the main area of
> interest for many Amber developers, but other messages on the mailing
> list indicate a great interest from the user side.
> Alternatively I may ask, if there are any other ways to tweak Amber16
> into running metadynamic simulations in the NVT ensemble on GPU, or if I
> need to bypass to OpenMM or GROMACS?

Amber has its own metadynamics, called "nfe" (non-equilibrium free energy),
which of course is not the same as PLUMED, but has attractive features.

I don't myself know of anyone trying to put PLUMED into pmemd, but maybe
someone on the list will pipe up. It doesn't look like(?!?) it should be very
hard to do this in the CPU version. We'd certainly consider contributions
along this line.

For the GPU, we are just now getting equilibrium free energy calculations
(such as TI, MBAR) into our code base. We'll be discussing other options at
the Amber developers meeting next week.

As an aside (and maybe you know this, but others on the list might not):
we are trying to improve connections between Amber and other codes. Users
can build their system in Amber, and equilibrate it and run simulations we
support in Amber. Then parmed can be used to port the system to OpenMM
or GROMACS if desired: see the "OpenMM" or "gromber" actions in parmed.

...hope this helps...others are welcome to chime in here!....dac

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Received on Mon Jan 29 2018 - 09:30:03 PST
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