[gmx-users] Accelerated MD in GROMACS

[James Starlight]

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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