[gmx-users] Replica exchange simulations more than number of processor

Sat Apr 15 15:03:24 CEST 2017

Dear gmx users,

Thank you very much for your useful discussions.

Best regards,
Mijee

On Sat, Apr 15, 2017 at 7:00 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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> Today's Topics:
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>    1. Re: Replica exchange simulations more than number of
>       processor (Thomas Piggot)
>    2. Re: Replica exchange simulations more than number of
>       processor (Christopher Neale)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 14 Apr 2017 20:06:29 +0100
> From: Thomas Piggot <t.piggot at soton.ac.uk>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Replica exchange simulations more than number
>         of processor
> Message-ID: <339c3321-fd12-7318-43b6-b41433f582fd at soton.ac.uk>
> Content-Type: text/plain; charset=gbk; format=flowed
>
> Have you thought about a more selective scaling of the interactions
> (i.e. HREX with only scalings applied for certain bits of the protein,
> not the complete thing as in REST2) so as to reduce the protein
> hydrophobicity at the lower lambda's? I've seen this selective scaling
> work well in other types of system to counteract broadly similar types
> of sampling issues at lower lambda's.
>
> Just a thought, it might not work well for what you are doing,
>
> Cheers
>
> Tom
>
> On 14/04/17 19:27, Christopher Neale wrote:
> > In REST2, the protein becomes way too hydrophobic as lambda is
> decreased. Just run a standard simulation at 300K, another at 600K and then
> another one at 300K with REST2 lambda=0.5 and you'll see what I mean.
> >
> > REST has a hidden barrier corresponding to the point at which water
> becomes a theta solvent and the exchange is very poor across that boundary,
> with globular replicas staying at higher lambda and extended replicas
> staying at lower lambda. However, with REST2, there is no such hidden
> barrier because water never gets anywhere near being a theta solvent. So in
> REST2 you get good exchange for all the wrong reasons.
> >
> > Work continues....
> >
> >
> > ________________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Thomas
> Piggot <t.piggot at soton.ac.uk>
> > Sent: 14 April 2017 14:16:26
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Replica exchange simulations more than number
> of processor
> >
> > Hi Chris,
> >
> > This is interesting. Do you have an idea why the sampling at low lambda
> > values isn't very good?
> >
> > Cheers
> >
> > Tom
> >
> > On 14/04/17 17:40, Christopher Neale wrote:
> >> What I have is only my own personal unpublished data. But add to that
> the number of years since REST2 came out and the low number of papers in
> which anybody did something useful with it and I'd say that suggests many
> others have tried and run into the same issues that I did (or maybe I'm
> just not reading the right papers, so please correct me if I am wrong).
> When my desired use failed I fell back to trp-cage folding in water and
> found the same things, so it's not like REST2 only fails for some exotic
> systems. Running 3 entirely separate repeats of regular T-REMD and 3 of
> REST2, I found that overall T-REMD is of similar or perhaps better
> efficiency (even though it has more replicas) compared to REST2. It's an
> on/off area of research for me, attempting to fix REST, but I still don't
> have a good answer for it.
> >>
> >>
> >> ________________________________________
> >> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Szil?rd
> P?ll <pall.szilard at gmail.com>
> >> Sent: 14 April 2017 12:26:41
> >> To: Discussion list for GROMACS users
> >> Subject: Re: [gmx-users] Replica exchange simulations more than number
> of       processor
> >>
> >> On Fri, Apr 14, 2017 at 5:51 PM, Christopher Neale <
> >> chris.neale at alum.utoronto.ca> wrote:
> >>
> >>> Just my 2 cents: REST2 doesn't work. The random walk is much better
> than
> >>> REST but the sampling efficiency at low lambda is now poor.
> >> Interesting. Is there any (published) data you could point to that
> supports
> >> this?
> >>
> >>
> >>> Your mileage may vary, but be aware that REST2 is not necessarily
> going to
> >>> be useful for all systems.
> >>> ________________________________________
> >>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> >>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Thomas
> >>> Piggot <t.piggot at soton.ac.uk>
> >>> Sent: 14 April 2017 09:23:35
> >>> To: gmx-users at gromacs.org
> >>> Subject: Re: [gmx-users] Replica exchange simulations more than number
> of
> >>> processor
> >>>
> >>> In addition, using another technique like REST2 may substantially
> reduce
> >>> the numbers of replica's you need. Still, more compute is definitely
> >>> recommended if you can get it.
> >>>
> >>> Cheers
> >>>
> >>> Tom
> >>>
> >>> On 14/04/17 12:48, Smith, Micholas D. wrote:
> >>>> You can try over assignment of cores, but that will be horribly slow.
> Or
> >>> use more than 1 node (if you can get it).
> >>>> ===================
> >>>> Micholas Dean Smith, PhD.
> >>>> Post-doctoral Research Associate
> >>>> University of Tennessee/Oak Ridge National Laboratory
> >>>> Center for Molecular Biophysics
> >>>>
> >>>> ________________________________________
> >>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> >>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of ?????
> >>> ????????? <b.mijiddorj at gmail.com>
> >>>> Sent: Friday, April 14, 2017 4:16 AM
> >>>> To: gromacs.org_gmx-users at maillist.sys.kth.se
> >>>> Subject: [gmx-users] Replica exchange simulations more than number of
> >>>    processor
> >>>> Dear gmx users,
> >>>>
> >>>> I would like to simulate folding of a peptides. I have only 12 core
> >>>> processor, and I assumed the number of replica using temperature
> >>> generator
> >>>> as following link
> >>>> http://folding.bmc.uu.se/remd/.
> >>>>
> >>>> The number of replica is about 60. How can I solve this problem? Can
> you
> >>>> advice me, please?
> >>>>
> >>>> Best regards,
> >>>> Mijee
> >>>> --
> >>>> 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.
> >>> --
> >>> Dr Thomas Piggot
> >>> Visiting Fellow
> >>> University of Southampton, UK.
> >>>
> >>> --
> >>> 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.
> > --
> > Dr Thomas Piggot
> > Visiting Fellow
> > University of Southampton, UK.
> >
> > --
> > 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.
>
> --
> Dr Thomas Piggot
> Visiting Fellow
> University of Southampton, UK.
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 14 Apr 2017 19:23:06 +0000
> From: Christopher Neale <chris.neale at alum.utoronto.ca>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Replica exchange simulations more than number
>         of processor
> Message-ID:
>         <SN2PR03MB2301C9C82BC8E629AC3F313CC5050 at SN2PR03MB2301.
> namprd03.prod.outlook.com>
>
> Content-Type: text/plain; charset="gb2312"
>
> Dear Thomas:
>
> Thanks for the suggestion. I have a way foward, I'm just being selective
> about what I share at this point. This thread got a bit side-tracked from
> my reason for posting, which was simply to help a user with a single
> 12-core node to realize that dedicating it to a 6-month REST2 simulation
> might not be a good idea.
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Thomas
> Piggot <t.piggot at soton.ac.uk>
> Sent: 14 April 2017 15:06:29
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Replica exchange simulations more than number of
> processor
>
> Have you thought about a more selective scaling of the interactions
> (i.e. HREX with only scalings applied for certain bits of the protein,
> not the complete thing as in REST2) so as to reduce the protein
> hydrophobicity at the lower lambda's? I've seen this selective scaling
> work well in other types of system to counteract broadly similar types
> of sampling issues at lower lambda's.
>
> Just a thought, it might not work well for what you are doing,
>
> Cheers
>
> Tom
>
> On 14/04/17 19:27, Christopher Neale wrote:
> > In REST2, the protein becomes way too hydrophobic as lambda is
> decreased. Just run a standard simulation at 300K, another at 600K and then
> another one at 300K with REST2 lambda=0.5 and you'll see what I mean.
> >
> > REST has a hidden barrier corresponding to the point at which water
> becomes a theta solvent and the exchange is very poor across that boundary,
> with globular replicas staying at higher lambda and extended replicas
> staying at lower lambda. However, with REST2, there is no such hidden
> barrier because water never gets anywhere near being a theta solvent. So in
> REST2 you get good exchange for all the wrong reasons.
> >
> > Work continues....
> >
> >
> > ________________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Thomas
> Piggot <t.piggot at soton.ac.uk>
> > Sent: 14 April 2017 14:16:26
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Replica exchange simulations more than number
> of processor
> >
> > Hi Chris,
> >
> > This is interesting. Do you have an idea why the sampling at low lambda
> > values isn't very good?
> >
> > Cheers
> >
> > Tom
> >
> > On 14/04/17 17:40, Christopher Neale wrote:
> >> What I have is only my own personal unpublished data. But add to that
> the number of years since REST2 came out and the low number of papers in
> which anybody did something useful with it and I'd say that suggests many
> others have tried and run into the same issues that I did (or maybe I'm
> just not reading the right papers, so please correct me if I am wrong).
> When my desired use failed I fell back to trp-cage folding in water and
> found the same things, so it's not like REST2 only fails for some exotic
> systems. Running 3 entirely separate repeats of regular T-REMD and 3 of
> REST2, I found that overall T-REMD is of similar or perhaps better
> efficiency (even though it has more replicas) compared to REST2. It's an
> on/off area of research for me, attempting to fix REST, but I still don't
> have a good answer for it.
> >>
> >>
> >> ________________________________________
> >> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Szil?rd
> P?ll <pall.szilard at gmail.com>
> >> Sent: 14 April 2017 12:26:41
> >> To: Discussion list for GROMACS users
> >> Subject: Re: [gmx-users] Replica exchange simulations more than number
> of       processor
> >>
> >> On Fri, Apr 14, 2017 at 5:51 PM, Christopher Neale <
> >> chris.neale at alum.utoronto.ca> wrote:
> >>
> >>> Just my 2 cents: REST2 doesn't work. The random walk is much better
> than
> >>> REST but the sampling efficiency at low lambda is now poor.
> >> Interesting. Is there any (published) data you could point to that
> supports
> >> this?
> >>
> >>
> >>> Your mileage may vary, but be aware that REST2 is not necessarily
> going to
> >>> be useful for all systems.
> >>> ________________________________________
> >>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> >>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Thomas
> >>> Piggot <t.piggot at soton.ac.uk>
> >>> Sent: 14 April 2017 09:23:35
> >>> To: gmx-users at gromacs.org
> >>> Subject: Re: [gmx-users] Replica exchange simulations more than number
> of
> >>> processor
> >>>
> >>> In addition, using another technique like REST2 may substantially
> reduce
> >>> the numbers of replica's you need. Still, more compute is definitely
> >>> recommended if you can get it.
> >>>
> >>> Cheers
> >>>
> >>> Tom
> >>>
> >>> On 14/04/17 12:48, Smith, Micholas D. wrote:
> >>>> You can try over assignment of cores, but that will be horribly slow.
> Or
> >>> use more than 1 node (if you can get it).
> >>>> ===================
> >>>> Micholas Dean Smith, PhD.
> >>>> Post-doctoral Research Associate
> >>>> University of Tennessee/Oak Ridge National Laboratory
> >>>> Center for Molecular Biophysics
> >>>>
> >>>> ________________________________________
> >>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> >>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of ?????
> >>> ????????? <b.mijiddorj at gmail.com>
> >>>> Sent: Friday, April 14, 2017 4:16 AM
> >>>> To: gromacs.org_gmx-users at maillist.sys.kth.se
> >>>> Subject: [gmx-users] Replica exchange simulations more than number of
> >>>    processor
> >>>> Dear gmx users,
> >>>>
> >>>> I would like to simulate folding of a peptides. I have only 12 core
> >>>> processor, and I assumed the number of replica using temperature
> >>> generator
> >>>> as following link
> >>>> http://folding.bmc.uu.se/remd/.
> >>>>
> >>>> The number of replica is about 60. How can I solve this problem? Can
> you
> >>>> advice me, please?
> >>>>
> >>>> Best regards,
> >>>> Mijee
> >>>> --
> >>>> 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.
> >>> --
> >>> Dr Thomas Piggot
> >>> Visiting Fellow
> >>> University of Southampton, UK.
> >>>
> >>> --
> >>> 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.
> > --
> > Dr Thomas Piggot
> > Visiting Fellow
> > University of Southampton, UK.
> >
> > --
> > 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.
>
> --
> Dr Thomas Piggot
> Visiting Fellow
> University of Southampton, UK.
>
> --
> 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.
>
> End of gromacs.org_gmx-users Digest, Vol 156, Issue 73
> ******************************************************
>