[gmx-users] strange lincs warning with version 4.6
Szilárd Páll
szilard.pall at cbr.su.se
Tue Dec 4 19:56:07 CET 2012
On Tue, Dec 4, 2012 at 5:09 PM, Mark Abraham <mark.j.abraham at 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.waltz at 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.waltz at physik.uni-**freiburg.de<
> sebastian.waltz at 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
> >>> --
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