Re: [gmx-users] REMD temperature spacing error
People often vary it to try to have an average exchange acceptance rate of a level they think is useful. But that is only a proxy for what they really want to achieve, which is replica flow, and it turns out that is a complex thing and often requires a irregular spacing anyway. Mark On Wed, Mar 13, 2013 at 6:02 PM, Nikunj Maheshwari wrote: > Sorry. I thought it was related to Boltzmann constt. > Then how is 'k' calculated ? > > On Wed, Mar 13, 2013 at 8:17 PM, Mark Abraham >wrote: > > > k is dimensionless. It does not relate to Boltzmann's constant. The > > exponential spacing it produces would lead to replica exchange rates that > > are constant over the T range, under certain assumptions (e.g. papers by > > David A Kofke). In practice, it normally would not lead to such rates. > > Whether constant exchange rate is even useful/meaningful is another > matter > > (e.g. papers by Walter Nadler & Ulrich Hansmann). > > > > Mark > > > > On Wed, Mar 13, 2013 at 12:49 PM, Nikunj Maheshwari < > > nixcrazyfor...@gmail.com> wrote: > > > > > I think determining k in the equation is not clear. How is it related > to > > a > > > system size? If k=1/(kb.t) [kb=boltzmann constt], then for a given > > starting > > > temperature, the temp. spacing will be the same. Is that correct? > > > > > > On Wed, Mar 13, 2013 at 5:02 PM, Mark Abraham < > mark.j.abra...@gmail.com > > > >wrote: > > > > > > > On Wed, Mar 13, 2013 at 11:24 AM, Nikunj Maheshwari < > > > > nixcrazyfor...@gmail.com> wrote: > > > > > > > > > Dear all. > > > > > > > > > > We are trying to run REMD on two proteins : 292 and 44 aa residues > > > using > > > > > GROMACS 4.6. > > > > > We are unable to obtain the temperature spacing using REMD > > temperature > > > > > generator (http://folding.bmc.uu.se/remd/) as it is giving myriad > > > > > temperature ranges (in the order of 150 for 250-550K range) > > > > > > > > > > > > > Sounds normal for the kind of system you seem to have. Higher numbers > > of > > > > degrees of freedom require closer temperature spacing. > > > > > > > > Is there any other way to determine the spacing? Can the equation > > > > > T(i)=T(0).e(k.i) be used, as we are unable to comprehend it? > > > > > > > > > > > > > Yes, but if you want exchanges to occur, there are constraints on the > > > size > > > > of k. What's so hard about T(i+1)=T(i)*k? > > > > > > > > Mark > > > > -- > > > > gmx-users mailing listgmx-users@gromacs.org > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > > * Please don't post (un)subscribe requests to the list. Use the > > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > -- > > > gmx-users mailing listgmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > * Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD temperature spacing error
Sorry. I thought it was related to Boltzmann constt. Then how is 'k' calculated ? On Wed, Mar 13, 2013 at 8:17 PM, Mark Abraham wrote: > k is dimensionless. It does not relate to Boltzmann's constant. The > exponential spacing it produces would lead to replica exchange rates that > are constant over the T range, under certain assumptions (e.g. papers by > David A Kofke). In practice, it normally would not lead to such rates. > Whether constant exchange rate is even useful/meaningful is another matter > (e.g. papers by Walter Nadler & Ulrich Hansmann). > > Mark > > On Wed, Mar 13, 2013 at 12:49 PM, Nikunj Maheshwari < > nixcrazyfor...@gmail.com> wrote: > > > I think determining k in the equation is not clear. How is it related to > a > > system size? If k=1/(kb.t) [kb=boltzmann constt], then for a given > starting > > temperature, the temp. spacing will be the same. Is that correct? > > > > On Wed, Mar 13, 2013 at 5:02 PM, Mark Abraham > >wrote: > > > > > On Wed, Mar 13, 2013 at 11:24 AM, Nikunj Maheshwari < > > > nixcrazyfor...@gmail.com> wrote: > > > > > > > Dear all. > > > > > > > > We are trying to run REMD on two proteins : 292 and 44 aa residues > > using > > > > GROMACS 4.6. > > > > We are unable to obtain the temperature spacing using REMD > temperature > > > > generator (http://folding.bmc.uu.se/remd/) as it is giving myriad > > > > temperature ranges (in the order of 150 for 250-550K range) > > > > > > > > > > Sounds normal for the kind of system you seem to have. Higher numbers > of > > > degrees of freedom require closer temperature spacing. > > > > > > Is there any other way to determine the spacing? Can the equation > > > > T(i)=T(0).e(k.i) be used, as we are unable to comprehend it? > > > > > > > > > > Yes, but if you want exchanges to occur, there are constraints on the > > size > > > of k. What's so hard about T(i+1)=T(i)*k? > > > > > > Mark > > > -- > > > gmx-users mailing listgmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > * Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD temperature spacing error
k is dimensionless. It does not relate to Boltzmann's constant. The exponential spacing it produces would lead to replica exchange rates that are constant over the T range, under certain assumptions (e.g. papers by David A Kofke). In practice, it normally would not lead to such rates. Whether constant exchange rate is even useful/meaningful is another matter (e.g. papers by Walter Nadler & Ulrich Hansmann). Mark On Wed, Mar 13, 2013 at 12:49 PM, Nikunj Maheshwari < nixcrazyfor...@gmail.com> wrote: > I think determining k in the equation is not clear. How is it related to a > system size? If k=1/(kb.t) [kb=boltzmann constt], then for a given starting > temperature, the temp. spacing will be the same. Is that correct? > > On Wed, Mar 13, 2013 at 5:02 PM, Mark Abraham >wrote: > > > On Wed, Mar 13, 2013 at 11:24 AM, Nikunj Maheshwari < > > nixcrazyfor...@gmail.com> wrote: > > > > > Dear all. > > > > > > We are trying to run REMD on two proteins : 292 and 44 aa residues > using > > > GROMACS 4.6. > > > We are unable to obtain the temperature spacing using REMD temperature > > > generator (http://folding.bmc.uu.se/remd/) as it is giving myriad > > > temperature ranges (in the order of 150 for 250-550K range) > > > > > > > Sounds normal for the kind of system you seem to have. Higher numbers of > > degrees of freedom require closer temperature spacing. > > > > Is there any other way to determine the spacing? Can the equation > > > T(i)=T(0).e(k.i) be used, as we are unable to comprehend it? > > > > > > > Yes, but if you want exchanges to occur, there are constraints on the > size > > of k. What's so hard about T(i+1)=T(i)*k? > > > > Mark > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD temperature spacing error
I think determining k in the equation is not clear. How is it related to a system size? If k=1/(kb.t) [kb=boltzmann constt], then for a given starting temperature, the temp. spacing will be the same. Is that correct? On Wed, Mar 13, 2013 at 5:02 PM, Mark Abraham wrote: > On Wed, Mar 13, 2013 at 11:24 AM, Nikunj Maheshwari < > nixcrazyfor...@gmail.com> wrote: > > > Dear all. > > > > We are trying to run REMD on two proteins : 292 and 44 aa residues using > > GROMACS 4.6. > > We are unable to obtain the temperature spacing using REMD temperature > > generator (http://folding.bmc.uu.se/remd/) as it is giving myriad > > temperature ranges (in the order of 150 for 250-550K range) > > > > Sounds normal for the kind of system you seem to have. Higher numbers of > degrees of freedom require closer temperature spacing. > > Is there any other way to determine the spacing? Can the equation > > T(i)=T(0).e(k.i) be used, as we are unable to comprehend it? > > > > Yes, but if you want exchanges to occur, there are constraints on the size > of k. What's so hard about T(i+1)=T(i)*k? > > Mark > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD temperature spacing error
On Wed, Mar 13, 2013 at 11:24 AM, Nikunj Maheshwari < nixcrazyfor...@gmail.com> wrote: > Dear all. > > We are trying to run REMD on two proteins : 292 and 44 aa residues using > GROMACS 4.6. > We are unable to obtain the temperature spacing using REMD temperature > generator (http://folding.bmc.uu.se/remd/) as it is giving myriad > temperature ranges (in the order of 150 for 250-550K range) > Sounds normal for the kind of system you seem to have. Higher numbers of degrees of freedom require closer temperature spacing. Is there any other way to determine the spacing? Can the equation > T(i)=T(0).e(k.i) be used, as we are unable to comprehend it? > Yes, but if you want exchanges to occur, there are constraints on the size of k. What's so hard about T(i+1)=T(i)*k? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
