[gmx-users] Accelerated MD in GROMACS

[James Starlight]

Ok, let's look on the things from another perspective:

Using Martini CG model I am modeling protein-protein binding initially
putting both proteins on the distance which is much bigger than
electrostatics and other non-bonded cut-offs defined by the force
field.
I need simple,  path in-depended method to speed-up the kinetics of
the association of the proteins which will allow to sample as much of
the potential binding poses as it would be possible.
I am non interesting in "true" thermodynamics within this system- I
need only to sample all of the possible binding poses - not
interesting in "adequate" fraction of population.
So what might be the best non-equilibrium approach which has already
implemented in GROMACS: which would first of all increase diffusion
processes within my system (not a conformation sampling)? Replica-
exchange?

J.

2016-07-05 20:46 GMT+02:00 Szilárd Páll <pall.szilard at gmail.com>:
> 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
>>>> >> --
>>>> >> Gromacs Users mailing list
>>>> >>
>>>> >> * Please search the archive at
>>>> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> >> posting!
>>>> >>
>>>> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>> >>
>>>> >> * For (un)subscribe requests visit
>>>> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> >> send a mail to gmx-users-request at gromacs.org.
>>>> >>
>>>> > --
>>>> > Gromacs Users mailing list
>>>> >
>>>> > * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> posting!
>>>> >
>>>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>> >
>>>> > * For (un)subscribe requests visit
>>>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.