I can't know why you observe things working, in part because you haven't said what's in this system :-) Pure inflexible water would be fine because the constraints setting doesn't matter to water.
Moreover, whether integration issues cause things to crash can depend on non-reproducible numerical effects, and the phase of the moon when you compiled can determine that. You may well have a real problem with GROMACS on GPUs that might be a GROMACS bug, but at the moment we can't be sure of that because of this other issue. You claim your settings are "rather typical." They are, except that constraints = hbonds and a 2fs time step are inconsistent because of the typical time scale of the vibration of the bonds between heavy atoms. This has been a frequent topic of conversation on this list, despite being knowledge at least a decade old - e.g. ref 118 of GROMACS manual, Feenstra et al. Mark On Tue, Dec 4, 2012 at 5:30 PM, sebastian < sebastian.wa...@physik.uni-freiburg.de> wrote: > On 12/04/2012 05:09 PM, Mark Abraham wrote: > >> 2fs is normally considered too large a time step for stable integration >> with only bonds to hydrogen constrained, so your observation of >> non-reproducible LINCS warnings is not indicative of some other problem. >> >> > > Sorry, but why is this whole setup running on my local desktop with GPUs? > As far as I know this is a rather typical set of parameters. > The only difference what I can think of is that gromacs was compiled with > intel and mkl libs on the cluster there as it was compiled with gcc and > fftw3 libs on the local desktop. > > Sebastian > > Also, if you ran your CPU-only calculations with nstlist=25 then AFAIK >> this >> works fine, but is inefficient. >> >> Mark >> >> On Tue, Dec 4, 2012 at 3:41 PM, sebastian< >> sebastian.wa...@physik.uni-**freiburg.de<sebastian.wa...@physik.uni-freiburg.de>> >> wrote: >> >> >> >>> On 11/23/2012 08:29 PM, Szilárd Páll wrote: >>> >>> >>> >>>> Hi, >>>> >>>> On Fri, Nov 23, 2012 at 9:40 AM, sebastian< >>>> sebastian.wa...@physik.uni-**f**reiburg.de <http://freiburg.de>< >>>> sebastian.waltz@**physik.uni-freiburg.de<sebastian.wa...@physik.uni-freiburg.de> >>>> >> >>>> >>>> wrote: >>>> >>>> >>>> >>>> >>>> >>>>> Dear GROMCS user, >>>>> >>>>> I installed the git gromacs VERSION 4.6-dev-20121117-7a330e6-dirty on >>>>> my >>>>> local desktop >>>>> >>>>> >>>>> >>>>> >>>> Watch out, the dirty version suffix means you have changed something in >>>> the >>>> source. >>>> >>>> >>>> >>>> >>>> >>>> >>>>> (2*GTX 670 + i7) and everything works as smooth as possible. The >>>>> outcomes >>>>> are very reasonable and match the outcome of the 4.5.5 version without >>>>> GPU >>>>> acceleration. On our >>>>> >>>>> >>>>> >>>>> >>>> What does "outcome" mean? If that means performance, than something is >>>> wrong, you should see a considerable performance increase (PME, >>>> non-bonded, >>>> bondeds have all gotten a lot faster). >>>> >>>> >>>> >>>> >>>> >>> With outcome I mean the trajectory not the performance. >>> >>> >>> >>> >>> >>>> >>>> >>>>> cluster (M2090+2*Xeon X5650) I installed the VERSION >>>>> 4.6-dev-20121120-0290409. Using the same .tpr file used for runs with >>>>> my >>>>> desktop I get lincs warnings that the watermolecules can't be settled. >>>>> >>>>> >>>>> >>>>> >>>>> >>>> The group kernels have not "stabilized" yet and there have been some >>>> fixes >>>> lately. Could you please the latest version and check again. >>>> >>>> >>>> >>>> >>> I installed the beta1 release and still the water can not be settled. >>> >>> Additionally, you could try running our regression tests suite ( >>> >>> >>>> git.gromacs.org/****regressiontests<http://git.gromacs.org/**regressiontests> >>>> <http://git.**gromacs.org/regressiontests<http://git.gromacs.org/regressiontests> >>>> >) >>>> >>>> to see if at least the tests pass with the >>>> binaries you compiled >>>> Cheers, >>>> -- >>>> Szilárd >>>> >>>> >>>> >>>> >>>> >>>> >>> Cheers, >>> >>> Sebastian >>> >>> >>> My .mdp file looks like: >>> >>> >>>> ; >>>>> title = ttt >>>>> cpp = /lib/cpp >>>>> include = -I../top >>>>> constraints = hbonds >>>>> integrator = md >>>>> cutoff-scheme = verlet >>>>> >>>>> ;define = -DPOSRES ; for possition restraints >>>>> >>>>> dt = 0.002 ; ps ! >>>>> nsteps = 100000000 \ >>>>> nstcomm = 25 ; frequency for center of mass >>>>> motion >>>>> removal >>>>> nstcalcenergy = 25 >>>>> nstxout = 100000 ; frequency for writting the >>>>> trajectory >>>>> nstvout = 100000 ; frequency for writting the >>>>> velocity >>>>> nstfout = 100000 ; frequency to write forces to >>>>> output trajectory >>>>> nstlog = 10000 ; frequency to write the log >>>>> file >>>>> nstenergy = 10000 ; frequency to write energies >>>>> to >>>>> energy file >>>>> nstxtcout = 10000 >>>>> >>>>> xtc_grps = System >>>>> >>>>> nstlist = 25 ; Frequency to update the neighbor >>>>> list >>>>> ns_type = grid ; Make a grid in the box and >>>>> only >>>>> check atoms in neighboring grid cells when constructing a new neighbor >>>>> rlist = 1.4 ; cut-off distance for the >>>>> short-range neighbor list >>>>> >>>>> coulombtype = PME ; Fast Particle-Mesh Ewald >>>>> electrostatics >>>>> rcoulomb = 1.4 ; cut-off distance for the >>>>> coulomb >>>>> field >>>>> vdwtype = cut-off >>>>> rvdw = 1.4 ; cut-off distance for the vdw >>>>> field >>>>> fourierspacing = 0.12 ; The maximum grid spacing for >>>>> the >>>>> FFT grid >>>>> pme_order = 6 ; Interpolation order for PME >>>>> optimize_fft = yes >>>>> pbc = xyz >>>>> Tcoupl = v-rescale >>>>> tc-grps = System >>>>> tau_t = 0.1 >>>>> ref_t = 300 >>>>> >>>>> energygrps = Protein Non-Protein >>>>> >>>>> Pcoupl = no;berendsen >>>>> tau_p = 0.1 >>>>> compressibility = 4.5e-5 >>>>> ref_p = 1.0 >>>>> nstpcouple = 5 >>>>> refcoord_scaling = all >>>>> Pcoupltype = isotropic >>>>> gen_vel = no;yes >>>>> gen_temp = 300 >>>>> gen_seed = -1 >>>>> >>>>> >>>>> Thanks a lot >>>>> >>>>> Sebastian >>>>> -- >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> http://lists.gromacs.org/******mailman/listinfo/gmx-users<http://lists.gromacs.org/****mailman/listinfo/gmx-users> >>>>> <htt**p://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>>> > >>>>> <htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/**listinfo/gmx-users> >>>>> <h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>> > >>>>> >>>>> >>>>> >>>>>> >>>>>> >>>>> * Please search the archive at http://www.gromacs.org/** >>>>> Support/Mailing_Lists/Search<**h**ttp://www.gromacs.org/**Support/**<http://www.gromacs.org/Support/**> >>>>> >>>>> Mailing_Lists/Search<http://**www.gromacs.org/Support/** >>>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search> >>>>> >>before >>>>> posting! >>>>> * Please don't post (un)subscribe requests to the list. 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