by the way, the machine has 4 Tesla K40m gpu, 32 xeon cpu with avx, and i ran: nohup ../../mdrun -deffnm npt15 -cpt 1 -cpnum &
On Tue, Nov 11, 2014 at 9:38 AM, Johnny Lu <johnny.lu...@gmail.com> 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? > > 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 gmx-users-requ...@gromacs.org.
