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-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 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.pig...@soton.ac.uk> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Replica exchange simulations more than number > of processor > Message-ID: <339c3321-fd12-7318-43b6-b41433f58...@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-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Thomas > Piggot <t.pig...@soton.ac.uk> > > Sent: 14 April 2017 14:16:26 > > To: gmx-us...@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-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Szil?rd > P?ll <pall.szil...@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.ne...@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-boun...@maillist.sys.kth.se < > >>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Thomas > >>> Piggot <t.pig...@soton.ac.uk> > >>> Sent: 14 April 2017 09:23:35 > >>> To: gmx-us...@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-boun...@maillist.sys.kth.se < > >>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of ????? > >>> ????????? <b.mijidd...@gmail.com> > >>>> Sent: Friday, April 14, 2017 4:16 AM > >>>> To: gromacs.org_gmx-users@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-requ...@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-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 > >> > >> * 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. > > -- > > 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-requ...@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.ne...@alum.utoronto.ca> > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] Replica exchange simulations more than number > of processor > Message-ID: > <SN2PR03MB2301C9C82BC8E629AC3F313CC5050@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-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Thomas > Piggot <t.pig...@soton.ac.uk> > Sent: 14 April 2017 15:06:29 > To: gmx-us...@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-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Thomas > Piggot <t.pig...@soton.ac.uk> > > Sent: 14 April 2017 14:16:26 > > To: gmx-us...@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-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Szil?rd > P?ll <pall.szil...@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.ne...@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-boun...@maillist.sys.kth.se < > >>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Thomas > >>> Piggot <t.pig...@soton.ac.uk> > >>> Sent: 14 April 2017 09:23:35 > >>> To: gmx-us...@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-boun...@maillist.sys.kth.se < > >>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of ????? > >>> ????????? <b.mijidd...@gmail.com> > >>>> Sent: Friday, April 14, 2017 4:16 AM > >>>> To: gromacs.org_gmx-users@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-requ...@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-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 > >> > >> * 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. > > -- > > 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-requ...@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-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. > > End of gromacs.org_gmx-users Digest, Vol 156, Issue 73 > ****************************************************** > -- 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.