The jump is much smaller though, and seems to decrease as I do more continuation.
These tripeptide simulations all use the same mdp file, without the shift potential, and with those ultra-conservative settings. http://oi57.tinypic.com/15f2mx1.jpg The order of restarts: Black -> Red -> Green -> Blue. Here is the example command I used to continue the simulation. grompp_d -f md_0_10.mdp -c md_0_9.tpr -t md_0_9.cpt -p topol.top -o md_0_10.tpr On Wed, Nov 12, 2014 at 10:16 AM, Johnny Lu <[email protected]> wrote: > This seems to have nothing to do with shifted potentials or gpu. > > I run a tripeptide double precisiion NVE simulation on a machine with xeon > cpu and without gpu. kill it, then continue it with the cpt file generated. > That energy jump still exists. > > On Tue, Nov 11, 2014 at 1:39 PM, Johnny Lu <[email protected]> wrote: > >> Going from non-shift to shifted potential changes the energy. So I was >> not surprised by the sudden jump of energy between step 0 and step 10 for >> the previous simulation (npt14). >> >> But the jump near step 0 for the current simulation (npt15) is not right. >> >> This is an equilibration run. >> >> I have just uploaded the files at http://redmine.gromacs.org/issues/1640 >> >> >> On Tue, Nov 11, 2014 at 10:54 AM, Mark Abraham <[email protected]> >> wrote: >> >>> On Tue, Nov 11, 2014 at 3:38 PM, Johnny Lu <[email protected]> >>> wrote: >>> >>> > Hi. >>> > >>> > I ran 30ns NPT with Potential-shift-Verlet on both potentials, >>> continuing >>> > from a NPT without Potential-shift-Verlet. The energy dropped from >>> -3e5 to >>> > -4e5, which is fine. >>> > >>> > After that, I continue the 30ns NPT with the same mdp file, except >>> with a >>> > longer run time (300ns). >>> > >>> > The total energy was -4e5 at step 0, and then -3e5 at step 5000, and >>> now at >>> > about 25 ns, it goes back to -3.5e5. Why the energy suddenly changed >>> after >>> > step 0? >>> > >>> >>> IIRC, the restart ought to compute the same energy on the initial >>> coordinates as it did at the end of the previous run, and even if there's >>> no re-computation on the same coordinates, obviously it should not jump >>> by >>> 1e5 in a few steps (or one? can't tell from the resolution). I would >>> think >>> that might be a bug in filling a data structure for the output, but >>> probably not one in the simulation itself. Please file an issue at >>> http://redmine.gromacs.org, tarballing all the relevant files, and I'll >>> try >>> to look at it. >>> >>> The long-time behaviour of both simulations is pretty suspect though. >>> Since >>> you're prepared to be ultra-conservative with your non-bonded and SETTLE >>> settings, I would explore using a 0.5fs time step (in normal and >>> ultra-conservative mode). Berendsen is not a good barostat algorithm for >>> production work, too... but I would not expect such a problem from its >>> use. >>> Perhaps more importantly, why are you turning off the long-range >>> dispersion >>> correction? >>> >>> Mark >>> >>> I used the same machine and same mixed precision gromacs 4.6.7 mdrun and >>> > grompp for both simulations. >>> > >>> > The plot of total energies for the two simulations: >>> > http://oi60.tinypic.com/ddmejd.jpg >>> > The two mdp files: http://oi58.tinypic.com/11980si.jpg >>> > >>> > The commands that I used for continuing the simulations: >>> > >>> > The previous simulation (npt14): >>> ../../sofware/gromacs-4.6.7/bin/grompp -f >>> > npt14.mdp -c npt13.tpr -t npt13_step22620750.cpt -o npt14.tpr >>> > >>> > The current simulation (npt15): ../../sofware/gromacs-4.6.7/bin/grompp >>> -f >>> > npt15.mdp -c npt14.tpr -t npt14_step30000000.cpt -o npt15.tpr >>> > >>> > Thanks. >>> > -- >>> > 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 [email protected]. >>> > >>> -- >>> 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 [email protected]. >>> >> >> > -- 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 [email protected].
