[gmx-users] strange lincs warning with version 4.6
sebastian
sebastian.waltz at physik.uni-freiburg.de
Tue Dec 4 17:30:47 CET 2012
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> 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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>>>>>
>>>>
>>>>
>>>>
>>>
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