sorry, i mean the lysozyme tutorial that i found there... On Wed, Sep 10, 2014 at 11:40 AM, Johnny Lu <johnny.lu...@gmail.com> wrote:
> hmm. If that is the case, I have two questions. > 1. Why gromacs doesn't adopt the method of measuring temperature as > described in the JCTC paper? > ( > https://www.deshawresearch.com/publications/Equipartition%20and%20the%20Calculation%20of%20Temperature%20in%20Biomolecular%20Simulations.pdf > ) > > 2. As the paper mentioned that using two thermostats can cause hot solvent > cold solute problem for the timesteps that we commonly use, why do your > lysozyme tutorial still use two thermostats? > ( > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/nvt.mdp > ) > > Thank you. > > > On Wed, Sep 3, 2014 at 4:07 PM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > >> Hi, >> >> It's impossible to say anything in the absence of a full description of >> the >> system and .mdp file - expecting good conservation can be a fool's errand. >> You could >> a) investigate the effect of time step on the difference in the observed >> temperature >> b) investigate the effect of the restraint strength constant on the >> temperature difference (it could be too large for the time step) >> c) try double precision (to see if the drift is intrinsic or due to >> accumulated rounding imprecision) >> d) assess which of the approximations you are making (drift from finite >> time step/model/implementation, static point charges, broken ergodicity, >> etc.) dominates the quality of your model physics. >> >> And consider that the measurement of temperature from momentum (as in >> GROMACS) is intrinsically flawed - see >> >> https://www.deshawresearch.com/publications/Equipartition%20and%20the%20Calculation%20of%20Temperature%20in%20Biomolecular%20Simulations.pdf >> >> Mark >> >> >> On Wed, Sep 3, 2014 at 6:21 PM, Johnny Lu <johnny.lu...@gmail.com> wrote: >> >> > I try the following: >> > >> > 0. Minimization >> > 1. NVT (100,000 steps of 2fs, 300K) >> > 2. NPT (100,000 steps of 2fs, 300K, V-rescale thermostat) >> > 3. NPT (5000 steps of 2fs, 308K, V-rescale thermostat) >> > 4. 9 x NVE (each 32768 steps of 0.75 fs) >> > 5. go to step 3. >> > >> > I plan to get rid of the first of nine NVE steps, as an NVE >> equilibration >> > step. >> > >> > At 0.75 fs, the total energy drop was about 0.03% per NVE step. >> > >> > Will that be fine? I am a bit worry that step 3 is too short. >> > I pick 308K because last time when I choose 300K for step 3, step 4 >> drops >> > to 292 K. >> > I hope that the NVE will be about 300K. >> > >> > May be I should look at the .edr file of step 3. >> > >> > Thanks. >> > >> > >> > On Wed, Sep 3, 2014 at 11:54 AM, Johnny Lu <johnny.lu...@gmail.com> >> wrote: >> > >> > > reading this post in maillist again: >> > > >> > >> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-May/071225.html >> > > >> > > I think that is exactly the same problem. >> > > >> > > >> > > On Wed, Sep 3, 2014 at 10:24 AM, Johnny Lu <johnny.lu...@gmail.com> >> > wrote: >> > > >> > >> Hi. >> > >> >> > >> After equilibrating with NVT (for 10,000 steps of 2fs) and then NPT >> > >> (10,000 steps of 2fs with V-rescale thermostat at 300K), when I run >> NVE >> > >> (0.5fs timesteps) with a harmonic restraint with force constant >> > 4184kJ/mol >> > >> rad^2, the temperature then fluctuate around 292 K ( >> > >> http://oi60.tinypic.com/sni5at.jpg) in gromacs 4.6.6. >> > >> >> > >> When I instead run NVE with same setting except without the >> constraint >> > >> after the two equilibration steps, the temperature stays around 300K. >> > >> >> > >> What is the cause of this drop of temperature to 292K? >> > >> >> > >> Thanks again. >> > >> >> > >> >> > >> >> > > >> > -- >> > 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.