Re: [gmx-users] Differences between 4.5.5 and 4.6.2-dev?
Dear Berk, der GMXers, On Apr 23, 2013, at 2:54 PM, Stefan Kesselheim wrote: > The temperature is 300.6, target temperature was 300. That should be fine. I > did check weaker fields and weaker thermostat coupling. Everything stayed > optimally consistent, within 4.5.5, however incompatible with 4.6.2. > I'm rerunning with cutoffs=1.4 now. I should get results by tomorrow. Now results are there and without twin-range I obtain consistent results between the GMX-versions. I'm now switching on twin-range and rerunning to check if the error does reappear. I don't know what would be better: Either I did something wrong in a very stupid way, or ... Thanks for your patience Stefan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Differences between 4.5.5 and 4.6.2-dev?
b71f8c8b75072. No GPU >> usage involved. 4.5.5 with "usual" mpi, 4.6.2 with thread-mpi. >> >> Can anybody think of an explanation? My hope would be that some default >> behaviour has changed between the versions. >> My short-term strategy is rerunning with a single cutoff of 1.4, an optimal >> choice of ewald_rtol (tuned with g_pme_error) and hope that the differences >> disappear. This however will take a while. >> Cheers and thanks in advance >> Stefan Kesselheim >> >> >> Here is the rest of my mdp file. >> >> define = -DPOSRES_P >> integrator = md >> tinit = 0 >> dt = 0.002 >> nsteps = 400 >> init_step = 0 >> comm_mode = None >> nstxout = 0 >> nstvout = 0 >> nstfout = 0 >> nstxtcout = 100 >> nstcheckpoint = 1 >> nstlog = 1 >> nstenergy = 1000 >> energygrps = POR SOL NA CL >> energygrp_excl = POR POR >> nstlist = 5 >> ns_type = grid >> pbc = xyz >> periodic_molecules = yes >> rlist = 0.9 >> domain-decomposition = yes >> coulombtype = PME >> rcoulomb-switch = 0 >> rcoulomb = 0.9 >> epsilon_r = 1 >> epsilon_rf = 1 >> vdwtype = Cut-Off >> rvdw-switch = 0. >> rvdw = 1.4 >> DispCorr = EnerPres >> table-extension = 1 >> energygrp_table = >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> ; EWALD/PME/PPPM parameters >> pme_order = 4 >> ewald_rtol = 1e-05 >> ewald_geometry = 3d >> epsilon_surface = 0 >> optimize_fft = no >> implicit_solvent = No >> tcoupl = v-rescale >> tc-grps = Water_and_ions POR >> tau-t = 5.0 5.0 >> ref-t = 300 300 >> nsttcouple = 1 >> pcoupl = no >> Pcoupltype = Isotropic >> tau-p = 1.0 >> compressibility = 4.5e-5 >> ref-p = 1.0 >> gen_vel = yes >> gen_temp = 300 >> gen_seed = 32293 >> ld_seed = 32293 >> E-x = >> E-xt = >> E-y = >> E-yt = >> E-z = 1 0.2 0 >> E-zt = >> constraints = hbonds >> >> >> --- >> Stefan Kesselheim >> Institute for Computational Physics >> Allmandring 3 >> +49 711 685 63630 >> 70184 Stuttgart >> kes...@icp.uni-stuttgart.de >> >> >> >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Differences between 4.5.5 and 4.6.2-dev?
Dear Gromacs users, a short disclaimer first: I'm new to using GROMACS and new to doing atomistic resolution modelling. If I'm doing anything very wrong, I'd be very happy to hear. I'm trying to simulate ion current in a nanopore. My nanopore consists of LJ particles positioned on the surface of a cylinder, that is closed with itself over PBC, thus my system is quasi-infinite. The pore is filled with SPC/E water and (in this particular simulation) 128 NA+ and CL- ions where I'm using the gromos53a6 ion parameters. An electric field is applied in the periodic direction. The current is then the sum of the distances traveled by all ions in a production run divided by the length of the box times +- 1 (depending on the ion species), divided by the simulation time. I noticed now the following: With GROMACS 4.5.5 and 4.6.2 I obtained different values for the currents; the NA ions travel faster in 4.6.2 while the Cl ions travel faster in 4.5.5. The difference is about 20% in both cases and it is statistically significant (5 or more sigma). I'm using PME for electrostatics as later a DNA molecule will be added, and the long range nature of electrostatics will most likely be quite important. I am using a twin range cutoff scheme with rlist= 0.9 rcoulomb = 0.9 rvdw = 1.4 and ewald_rtol = 1e-05 and the default fourier_spacing (which should be 1.2 nm). According to g_pme_error this choice is not particularly smart (I will do better, I promise) but however should not explain any differences between the two versions. Comparing the gmxdump output of both tprs i noticed the following differences: 4.6.2 | 4.5.5 verlet-buffer-drift = 0.005| verlet-buffer-drift = 0 fourierspacing = 0.12 | fourierspacing = 0 dihre-fc = 0|dihre-fc = 1000 These parameters are my top candidates to explain differences, but I have attached the rest of the production run mdp below. My 4.5.5 version was the official one compiled on our local supercomputer (by the admins) and my 4.6.2 version is from the git repository, branch release-4.6, last commit 873b98540a47a5727e69342117ab71f8c8b75072. No GPU usage involved. 4.5.5 with "usual" mpi, 4.6.2 with thread-mpi. Can anybody think of an explanation? My hope would be that some default behaviour has changed between the versions. My short-term strategy is rerunning with a single cutoff of 1.4, an optimal choice of ewald_rtol (tuned with g_pme_error) and hope that the differences disappear. This however will take a while. Cheers and thanks in advance Stefan Kesselheim Here is the rest of my mdp file. define = -DPOSRES_P integrator = md tinit= 0 dt = 0.002 nsteps = 400 init_step= 0 comm_mode= None nstxout = 0 nstvout = 0 nstfout = 0 nstxtcout= 100 nstcheckpoint= 1 nstlog = 1 nstenergy= 1000 energygrps = POR SOL NA CL energygrp_excl = POR POR nstlist = 5 ns_type = grid pbc = xyz periodic_molecules = yes rlist= 0.9 domain-decomposition = yes coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 epsilon_r= 1 epsilon_rf = 1 vdwtype = Cut-Off rvdw-switch = 0. rvdw = 1.4 DispCorr = EnerPres table-extension = 1 energygrp_table = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no implicit_solvent = No tcoupl = v-rescale tc-grps = Water_and_ions POR tau-t= 5.0 5.0 ref-t= 300 300 nsttcouple = 1 pcoupl = no Pcoupltype = Isotropic tau-p= 1.0 compressibility = 4.5e-5 ref-p= 1.0 gen_vel = yes gen_temp = 300 gen_seed = 32293 ld_seed = 32293 E-x = E-xt = E-y = E-yt = E-z = 1 0.2 0 E-zt = constraints = hbonds ------- Stefa
