ewald_rtol of 1e-9 is a very long way from the normal range of values, and your other electrostatics settings seem pretty normal. I'd expect these results to be of doubtful value, but I am surprised to see that/if there is a marked different with acceleration type. I suggest you try a normal simulation protocol and see how you go.
Mark On Fri, Aug 30, 2013 at 7:31 PM, Ali Sinan Saglam <asinansag...@gmail.com> wrote: > Hi Mark, > > I have tried GCC 4.7.1, 4.7.2 and ICC 13 (with and without MKL, my > colleague also tried double precision) compilers, all showed the same > behavior. > > I will add the .mdp file I have used but the problem consists for all input > files my colleagues tried (they had their own input files, independent to > me). For example the first graph is Barnase - Barstar in a large box > (~100,000 atoms, explicit tip3p waters, neutralized and a small amount of > salt, roughly 60-70 atoms of NaCl) and the mdp file used was; > ;##################################################### INTEGRATOR > ###################################################### > integrator = md ; Molecular > dynamics > dt = 0.002 ; Timestep (ps) > nsteps = 500000 ; Simulation > duration (timesteps) > nstcomm = 1000 ; Center of > mass motion removal interval (timesteps) > comm-grps = system ; Remove center > of mass motion of system > ;###################################################### ENSEMBLE > ####################################################### > Pcoupl = no ; Disable > barostat > tcoupl = no ; Disable > thermostat > ;################################################ BONDED INTERACTIONS > ################################################## > constraints = hbonds ; Disable > constraints > constraint_algorithm = LINCS ; Constrain > bonds using LINCS > lincs_iter = 1 ; Number of > LINCS iterations > ;############################################### NONBONDED INTERACTIONS > ################################################ > coulombtype = PME ; Switch/PME > long-range electrostatics > fourierspacing = 0.1 > pme_order = 4 > ewald_rtol = 0.000000001 > pbc = xyz ; Periodic > boundary condition > rcoulomb = 1.00 ; Short-range > electrostatic cutoff (nm) > ;rcoulomb_switch = 0.9 ; Short-range > electrostatic switch cutoff (nm) > vdwtype = Switch ; Switch van > der Waals interactions > rvdw = 0.9 ; Van der Waals > cutoff (nm) > rvdw_switch = 0.8 ; Van der Waals > switch cutoff (nm) > DispCorr = EnerPres ; Long-range > dispersion correction to energy and pressure > ns_type = grid ; Update > neighbor list using grid > nstlist = 10 ; Neighbor list > update interval (timesteps) > rlist = 1.00 ; Neighbor list > cut-off (nm) > continuation = yes > ;####################################################### OUTPUT > ######################################################## > nstlog = 500 ; Energy log > output interval (timesteps) > nstenergy = 500000 ; Energy output > interval (timesteps) > nstxout = 500000 ; > Full-resolution trajectory output interval (timesteps) > nstvout = 500000 ; > Full-resolution velocity output interval (timesteps) > nstfout = 500000 ; > Full-resolution force output interval (timesteps) > nstxtcout = 500 ; > Reduced-resolution trajectory output interval (timesteps) > xtc-precision = 10000 ; > Reduced-resolution trajectory output precision > > While the second graph is for EG5 (~130,000 atoms I believe, I don't have > the exact number but I remember that it's a bigger system than mine, same > water model). I'm unsure what my 3rd colleague tested but had similar > results (his system heated to 400+K) and we didn't share any input files. > All conserved energy fine with SSE instruction set (my results were losing > energy with 1.1kcal/mol.ps) > > Best, > Ali Sinan Saglam > > > On Fri, Aug 30, 2013 at 12:03 PM, Mark Abraham > <mark.j.abra...@gmail.com>wrote: > >> With what compiler? (e.g. consult mdrun -version) There are many known >> bugs in early point versions of each minor release of gcc, for >> example. This is why the installation instructions stress getting the >> latest version of your compiler. >> >> Otherwise, what is your .mdp file and simulation system contents? >> >> Mark >> >> On Fri, Aug 30, 2013 at 5:48 PM, Ali Sinan Saglam >> <asinansag...@gmail.com> wrote: >> > Hi, >> > >> > I have been running some energy conservation tests with GMX4.6.3 and had >> > encountered some issues when using the AVX-256 instruction set. >> > >> > I first noticed that my systems were freezing on a cluster that uses >> > Sandy-bridge CPUs and did not on a different cluster using SSE. After >> > realizing that the problems were not in my configuration and setup I >> > started compiling multiple copies of Gromacs and saw that only the >> AVX-256 >> > compiled binaries showed this behavior. >> > >> > After a few colleagues reproduced the same results, I'm now pretty sure >> > this is the case. Two colleagues started completely independently and >> > reproduced the same behavior on 2 different clusters and 2 desktop >> machines >> > (all sandy-brige, in all cases AVX yielded really weird temperatures, >> > sometimes exponential freezing sometimes heating etc.). >> > >> > Gromacs was compiled with -DGMX_CPU_ACCELERATION=AVX or =SSE4.1 (or any >> > version of SSE) and that was the only difference between the two >> binaries. >> > The method of simulation was exactly the same outside of the mdrun that >> was >> > used. The temperature results from my simulations can be seen here; >> > https://www.dropbox.com/s/ul7g0fb4il17wxm/avx_sse_temp.png >> > Another example with a different person reproducing the results; >> > https://www.dropbox.com/s/x7mr3kcgmvd78ie/adam_avx_sse_temp.png >> > >> > Cmake command was; >> > cmake SOURCE -DGMX_BUILD_OWN_FFTW=on -DGMX_OPENMM=off -DGMX_MPI=off >> > -DGMX_GPU=off -DGMX_THREAD_MPI=on -DGMX_CPU_ACCELERATION=AVX (or SSE4.1) >> > (also tried THREAD_MPI=off, similar results) >> > >> > Also all builds passed regression tests. >> > >> > I just wondered if this is a known problem or are we making a mistake >> while >> > compiling? >> > >> > Best, >> > Ali Sinan Saglam >> > -- >> > 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 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 >> > > > > -- > Ali Sinan Saglam > Graduate Student in Chemistry > Chong Lab, Room 338, Eberly Hall > University of Pittsburgh > Pittsburgh, PA 15260 > -- > 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 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
