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.
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> 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-**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>) >> 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> >>> > >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<h**ttp://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. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> >>> >> > -- > gmx-users mailing list gmx-users@gromacs.org > http://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<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? 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