Thus, what is your question now? :-) The total energy must remain conserved at all times. That's it.
Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sun, Oct 12, 2014 at 2:45 AM, Johnny Lu <johnny.lu...@gmail.com> wrote: > I tried PME and then potential-shift-verlet for Van der Waals. The energy > is still not constant in mixed precision gromacs 5.0.1 NVE run on 12 xeon > cpu without gpu. Those were nearly the last few things that I knew that I > can try in mixed precision. The system has ~165 amino acid, ~9000 water, > and 3 Cl- ion in a truncated rhombic dodecahedron box. Total energy of the > following simulation drift constantly down. This production run was a > continuation of ~300ns npt and ~300ns nvt. The PME grid was 80x80x80. > > ; Run parameters > integrator = md-vv ; leap-frog integrator > nsteps = 150000000 ; 1 ns > dt = 0.0005 ; 0.5 fs > > ;NVE > ; nstcomm = 500 ; remove center of mass motion to reduce energy and > temp. drift. (seems less drift without this) > shake-tol = 0.000001 ; shake tolerance. > verlet-buffer-tolerance = 0.00000005 > > ;Output control > nstenergy = 20 ; save energies every 1.0 ps > > nstlog = 100 ; update log file every 0.2 ps > ; Bond parameters > continuation = yes ; Restarting after NVT > constraint_algorithm = lincs ; holonomic constraints > constraints = all-bonds ; all bonds (even heavy atom-H bonds) > constrained > lincs_iter = 2 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > ; Neighborsearching > ns_type = grid ; search neighboring grid cells > nstlist = 5 ; 10 fs > > vdw-modifier = Potential-shift-Verlet; > > rlist = 1.1 ; short-range neighborlist cutoff (in nm) > rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) > rvdw = 1.0 ; short-range van der Waals cutoff (in nm) > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for long-range > electrostatics > pme_order = 6 ; cubic interpolation > fourierspacing = 0.1 ; grid spacing for FFT > > ; Temperature coupling is off > tcoupl = no ; modified Berendsen thermostat > ; Pressure coupling is off > pcoupl = no > > refcoord_scaling = com > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > ; Dispersion correction > DispCorr = EnerPres ; account for cut-off vdW scheme > ; Velocity generation > gen_vel = no ; Velocity generation is off > cutoff-scheme = Verlet > > > I guess the energy leakage when no thermostat is used doesn't mean the > distribution of conformation is incorrect when a thermostat is used. > Since double precision run is stable while single precision is not, the > energy leakage is caused by numerical error of the computer operation and > algorithm instead of the physics or conformation of the setup. (only the > precision changed. the mdp files were the same.) > > I also guess that the majority of simulations in published paper would have > such constant drop/rise of total energy if the thermostat is switched off. > ( Is this true??? ) > > When the Amber99ff-ILDN force field is made, NPT and NVT is used, instead > of NVE [http://dx.doi.org/10.1002%2Fprot.22711] > > The Amber lipid 14 forcefield uses NPT to create the parameters. In one of > the validations, they ran NPT followed by NVE to calculate diffusion > coefficient. The tolerance was more stringent in the NVE part than the NPT > part. The plot of energy v.s. time seems to be not in the paper. [ > http://pubs.acs.org/doi/full/10.1021/ct4010307] > > Dynamics is another matter. Langevin thermostats removes momentum transfer > and changes the rate dynamics, despite it samples the canonical ensemble > ... if the system is ergodic in practice. Two different simulations can > converge, if the string of random numbers used in langevin thermostats is > the same. I'm not sure about V-rescaling. > > I agree that all thermostats and barostats likely cause some artifacts in > dynamics. > > > On Sat, Oct 11, 2014 at 5:29 PM, Dr. Vitaly Chaban <vvcha...@gmail.com> > wrote: > >> Well, if it does not conserve total energy, than such a computational >> experiment is not reliable. This is a sad truth. >> >> Philosophically, you have two options here. Either you accept that >> energy leakage is significant and then you must fight against it >> (smaller time-step, double precision, constraints, etc), or -- on the >> contrary -- you say that energy loss can be neglected and proceed "as >> is". >> >> My personal rule is if the system does not lose more than 2% of total >> energy during an entire run, the result is acceptable. I can be >> criticized for this voluntary assumption, obviously. >> >> Anyway, tricks with T-coupling constitute a very bad idea in this >> case. You basically try to mask the energy leakage problem with the >> thermostat. Thermostat never removes the problem itself. >> >> >> Dr. Vitaly V. Chaban >> >> Виталий Витальевич ЧАБАН >> >> >> On Sat, Oct 11, 2014 at 11:12 PM, Johnny Lu <johnny.lu...@gmail.com> >> wrote: >> > I tried NVE on single precision gromacs 4.6.7 with and without GPU. >> > The energy either drift down or up, depending on the mdp file, and the >> drift >> > seems linear. >> > >> > Linear fit says that if I run 100 ns simulation, at the end the energy is >> > doubled. >> > >> > If I use double precision gromacs, the drift seems insignificant over >> 100 ns >> > simulation by linear regression fitting on a 300 ps run. >> > But double precision gromacs can't use gpu and is much slower than single >> > precision gromacs. >> > >> > On Sat, Oct 11, 2014 at 4:33 PM, Dr. Vitaly Chaban <vvcha...@gmail.com> >> > wrote: >> >> >> >> I also cannot get why not to just turn off the thermostat... >> >> >> >> If energy transfer phenomena are in focus, NVE is an ensemble of >> >> choice, no matter which relaxation constant is used for the T-coupling >> >> algorithm. >> >> >> >> >> >> Dr. Vitaly V. Chaban >> >> >> >> Виталий Витальевич ЧАБАН >> >> >> >> >> >> On Sat, Oct 11, 2014 at 6:32 PM, Antonio Baptista <bapti...@itqb.unl.pt >> > >> >> wrote: >> >> > Then, run true NVE, for the reasons we already pointed. >> >> > >> >> > On Sat, 11 Oct 2014, Johnny Lu wrote: >> >> > >> >> >> For dynamics with correct rate and correct fluctuation. >> >> >> >> >> >> On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban < >> vvcha...@gmail.com> >> >> >> wrote: >> >> >> >> >> >>> what is it needed for? >> >> >>> >> >> >>> >> >> >>> >> >> >>> Dr. Vitaly V. Chaban >> >> >>> >> >> >>> Виталий Витальевич ЧАБАН >> >> >>> >> >> >>> >> >> >>> On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu <johnny.lu...@gmail.com> >> >> >>> wrote: >> >> >>> > Hi. >> >> >>> > >> >> >>> > Is it a good idea to mimic NVE by a NVT simulation with a large >> >> >>> temperature >> >> >>> > coupling time constant, to reduce the effect of the thermostat ? >> >> >>> > >> >> >>> > If I use V-rescale thermostat, what artifacts will the simulation >> >> >>> > get >> >> >>> > if >> >> >>> I >> >> >>> > use a large coupling time (say, 500 ps) and single precision >> gromacs >> >> >>> > ? >> >> >>> > >> >> >>> > Thank you. >> >> >>> > -- >> >> >>> > 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? 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