Re: [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 :
> On Tue, Jul 5, 2016 at 3:56 PM, James Starlight  
> 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 :
>>> 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 
>>> 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 :
 > 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 
 > 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-requ...@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
 

Re: [gmx-users] Accelerated MD in GROMACS

[Szilárd Páll]

On Tue, Jul 5, 2016 at 3:56 PM, James Starlight  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 :
>> 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 
>> 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 :
>>> > 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 
>>> > 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-requ...@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-requ...@gromacs.org.
>>> --
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>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
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>>>
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Re: [gmx-users] Accelerated MD in GROMACS

[Catarina A. Carvalheda dos Santos]

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 :
> 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 
> 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 :
>> > 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 
>> > 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-requ...@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-requ...@gromacs.org.
>> --
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>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
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Re: [gmx-users] Accelerated MD in GROMACS

[James Starlight]

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 :
> 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 
> 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 :
>> > 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 
>> > 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-requ...@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-requ...@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
>>
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>>
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Re: [gmx-users] Accelerated MD in GROMACS

[Mark Abraham]

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 
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 :
> > 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 
> > 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-requ...@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
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [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 :
> 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 
> 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
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Re: [gmx-users] Accelerated MD in GROMACS

[Mark Abraham]

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 
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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[gmx-users] Accelerated MD in GROMACS

[James Starlight]

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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Re: [gmx-users] Accelerated MD

[Patrick Fuchs]

Hi Doug,
I recently read a good review on ABF 
http://pubs.acs.org/doi/abs/10.1021/jp506633n. It's focused on ABF but 
there's a section which compares ABF to other techniques.
While I'm at it, are there any plans from gromacs devs to implement ABF 
in gromacs?

Best,

Patrick

Le 20/10/2014 22:33, Douglas Houston a écrit :

Hi all,

Can anyone recommend a book or (preferably) review article summarising
the various accelerated MD methods commonly used in protein/peptide
simulation these days? e.g. ABF, PLUMED, REMD, aMD etc. etc. I can read
about each individually but I could use a comprehensive but concise
comparison of their pros/cons and most popular applications.

cheers,
Doug


_
Dr. Douglas R. Houston
Lecturer
Institute of Structural and Molecular Biology
Room 3.23, Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358
http://tinyurl.com/douglasrhouston





--
___
Patrick FUCHS
Dynamique des membranes et trafic intracellulaire
Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot
Bâtiment Buffon, 15 rue Hélène Brion, 75013 Paris
Tel :  +33 (0)1 57 27 80 05 - Fax : +33 (0)1 57 27 81 35
E-mail address: patrick.fu...@univ-paris-diderot.fr
Web Site: http://www.dsimb.inserm.fr/~fuchs
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[gmx-users] Accelerated MD

[Douglas Houston]

Hi all,

Can anyone recommend a book or (preferably) review article summarising  
the various accelerated MD methods commonly used in protein/peptide  
simulation these days? e.g. ABF, PLUMED, REMD, aMD etc. etc. I can  
read about each individually but I could use a comprehensive but  
concise comparison of their pros/cons and most popular applications.


cheers,
Doug


_
Dr. Douglas R. Houston
Lecturer
Institute of Structural and Molecular Biology
Room 3.23, Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358
http://tinyurl.com/douglasrhouston



--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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