[gmx-users] strange lincs warning with version 4.6
Thomas Piggot
t.piggot at soton.ac.uk
Tue Dec 4 18:48:26 CET 2012
Hi Mark,
I am not so sure regarding your point about a 2 fs timestep and
constraints = hbonds. Typical bond vibration between heavy atoms has
roughly a 20 fs period (see table I of the Feenstra et al. paper you
mentioned previously), so a timestep of 2 fs should be fine with
constraints = hbonds. As to whether this is more appropriate than
constraining all bonds is a different matter, but I do not believe the
simulations should have problems because of this setting.
Cheers
Tom
Mark Abraham wrote:
> 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.waltz at 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.waltz at physik.uni-**freiburg.de<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-**f**reiburg.de <http://freiburg.de><
>>>>> sebastian.waltz@**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>
>>>>> <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
>>>>>> --
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--
Dr Thomas Piggot
University of Southampton, UK.
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