[gmx-users] Accelerated MD in GROMACS

Tue Jul 5 18:54:27 CEST 2016

Hi,

What do you mean by "it gives more predicable results compared to flooding"?
I was actually going to propose that option.
If anything, the flooding potential applied  in conformational flooding is
more meaningful than a non-specific boost potential (to the dihedral and/or
total potential) that depends on a threshold value which calculation is not
always straightforward.

I'm not sure if conformational flooding is still part of the latest
versions (haven't check the release notes yet), but in principle there's no
reason not to. Also I'm not sure if it works with martini though.

Regards,

Hi Mark,

amd + martini is very popular aproach used by biologists and
biothechnologist becasue of its simplicity compared to umbrella
sampling or IT, alternatively it gives more predicable results
compared to flooding which has implemented in Gromacs.  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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