On Tue, Dec 4, 2012 at 5:09 PM, Mark Abraham <mark.j.abra...@gmail.com>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. > > Also, if you ran your CPU-only calculations with nstlist=25 then AFAIK this > works fine, but is inefficient. > With the verlet scheme when running on GPUs and/or at high parallelization nstlist = 25, even up to 50 can give higher performance (and this is safe to do because the buffer is automatically adjusted). -- Szilárd > > 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? Read 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 > * 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