Re: [gmx-users] Lambda Weights from Expanded Ensemble Code
Okay, thanks, I created a redmine request: #3304 On Wed, Jan 15, 2020 at 11:23 PM Michael Shirts wrote: > The simulated tempering options haven't been as well tested as the > hamiltonian expanded ensemble version. The weights SHOULD be showing up in > the column that says -nan, but clearly they aren't. If you file a redmine > issue, I may be able to take a look, but it might take a while to address. > > On Wed, Jan 15, 2020 at 8:52 PM Daniel Kozuch > wrote: > > > Hello, > > > > I am interested in using simulated tempering in GROMACS (2019.5) under > the > > expanded ensemble options. Is there a way to monitor the ensemble weights > > as the simulation progresses? I think in theory they are supposed to be > > printed out in the log file, but it is only printing 0, -nan, and inf: > > > > MC-lambda information > > N Temp.(K)Count G(in kT) dG(in kT) > > ... > > 36 359.105 118 -nan -nan << > > 37 366.880 96 -nan -nan > > 38 374.852 107 -nan -nan > > 39 383.026 129 -nan -nan > > 40 391.407 166 -nan -nan > > 41 400.000 199 -nan0.0 > > > > Here are my relevant mdp settings: > > simulated-tempering = yes > > nstexpanded = 500 > > simulated-tempering-scaling = exponential > > lmc-stats = metropolis-transition > > lmc-move= metropolis > > > > Any suggestions? > > > > Best, > > Dan Kozuch > > -- > > 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.
Re: [gmx-users] Lambda Weights from Expanded Ensemble Code
The simulated tempering options haven't been as well tested as the hamiltonian expanded ensemble version. The weights SHOULD be showing up in the column that says -nan, but clearly they aren't. If you file a redmine issue, I may be able to take a look, but it might take a while to address. On Wed, Jan 15, 2020 at 8:52 PM Daniel Kozuch wrote: > Hello, > > I am interested in using simulated tempering in GROMACS (2019.5) under the > expanded ensemble options. Is there a way to monitor the ensemble weights > as the simulation progresses? I think in theory they are supposed to be > printed out in the log file, but it is only printing 0, -nan, and inf: > > MC-lambda information > N Temp.(K)Count G(in kT) dG(in kT) > ... > 36 359.105 118 -nan -nan << > 37 366.880 96 -nan -nan > 38 374.852 107 -nan -nan > 39 383.026 129 -nan -nan > 40 391.407 166 -nan -nan > 41 400.000 199 -nan0.0 > > Here are my relevant mdp settings: > simulated-tempering = yes > nstexpanded = 500 > simulated-tempering-scaling = exponential > lmc-stats = metropolis-transition > lmc-move= metropolis > > Any suggestions? > > Best, > Dan Kozuch > -- > 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.
[gmx-users] Lambda Weights from Expanded Ensemble Code
Hello, I am interested in using simulated tempering in GROMACS (2019.5) under the expanded ensemble options. Is there a way to monitor the ensemble weights as the simulation progresses? I think in theory they are supposed to be printed out in the log file, but it is only printing 0, -nan, and inf: MC-lambda information N Temp.(K)Count G(in kT) dG(in kT) ... 36 359.105 118 -nan -nan << 37 366.880 96 -nan -nan 38 374.852 107 -nan -nan 39 383.026 129 -nan -nan 40 391.407 166 -nan -nan 41 400.000 199 -nan0.0 Here are my relevant mdp settings: simulated-tempering = yes nstexpanded = 500 simulated-tempering-scaling = exponential lmc-stats = metropolis-transition lmc-move= metropolis Any suggestions? Best, Dan Kozuch -- 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.
