[gmx-users] Accelerated MD in GROMACS

[Szilárd Páll]

On Tue, Jul 5, 2016 at 3:56 PM, James Starlight <jmsstarlight at gmail.com> wrote:
> Hi Mark,
>
> amd + martini is very popular aproach used by biologists and
> biothechnologist becasue of its simplicity compared to umbrella
> sampling or IT,

What about simplicity vs robustness?

Robustness is one of the key and attractive aspects of AWH and it's a
feature that sometimes seems to get overlooked and traded for
simplicity.

> alternatively it gives more predicable results
> compared to flooding which has implemented in Gromacs.

Mark was referring to AWH, not flooding.

> Finally the
> aMD is much easily calibrated for particular cases compared to
> replica-exchange method. Some selected publications regarding aMD in
> GPCR field for instance:
>  http://www.pnas.org/content/110/27/10982.short
> http://pubs.rsc.org/is/content/articlehtml/2014/cp/c3cp53962h
> http://pubs.acs.org/doi/abs/10.1021/ct300284c
>
> Regards
>
>
> J.
>
> 2016-07-05 15:42 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
>> Hi,
>>
>> Absolutely. It's merely a question of prioritising limited resources. For
>> example, one has to be able to answer "why should one use aMD rather than
>> AWH?" in order to consider implementing a new method. Then it has to impact
>> a bunch of people, or be immediately useful to the developer / their
>> colleagues, in order for someone to choose to pay for the work.
>>
>> Mark
>>
>> On Tue, Jul 5, 2016 at 3:29 PM James Starlight <jmsstarlight at gmail.com>
>> wrote:
>>
>>> Hello Mark,
>>>
>>> probably to implement of aMD in Gromacs will be very good as well:  it
>>> will allow to use this protocol with the CG martini systems - where to
>>> accelerate sampling of diffusion using double boost approach of amd
>>> seems very attractive option for modeling of protein-protein binding
>>> for instance. Compared to others MD packages - combining of those
>>> points  will be only available for GROMACS users ;-)
>>>
>>> James
>>>
>>> 2016-07-05 13:00 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
>>> > Hi,
>>> >
>>> > In general, one should look at the release notes of software to see what
>>> > new features were added in a version. This will tend to be findable with
>>> > Google also :-)
>>> >
>>> > Accelerated MD has never been implemented to my knowledge. It would
>>> > probably be fairly easy, but so far nobody with a suitable problem has
>>> > wanted to write the code. Alternatively, AWH
>>> > http://scitation.aip.org/content/aip/journal/jcp/141/4/10.1063/1.4890371
>>> is
>>> > implemented, and will likely be available shortly for people to use,
>>> based
>>> > on the upcoming GROMACS 2016, but won't be formally part of the 2016
>>> > GROMACS release.
>>> >
>>> > Mark
>>> >
>>> > On Tue, Jul 5, 2016 at 12:47 PM James Starlight <jmsstarlight at gmail.com>
>>> > wrote:
>>> >
>>> >> Dear Gromacs users!
>>> >>
>>> >> I wonder t ask whether the aMD was implemented within GMX-5 ?  I am
>>> >> looking for the non-equilibrium md protocol with the possibilities to
>>> >> apply one or two boosts on the system to accelerate some diffusion
>>> >> events within it.
>>> >>
>>> >> Thanks !
>>> >>
>>> >> James
>>> >> --
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