[gmx-users] Re: Note on oscillation period / time step
Justin A. Lemkul
jalemkul at vt.edu
Thu Dec 2 20:05:30 CET 2010
Robin C. Underwood wrote:
> Thanks for all the responses. After rechecking my top and manually inputting
> the [ ...types ] fields, the note remains. It is not clear to me whether I need
> to modify my top file or add some additional constraint (either in the top or
> mdp). Is it OK to have a bond oscillation period of this magnitude relative to
> my timestep? I've not seen this note in previous versions.
>
Please see the manual, sections 1.2 and 6.5 in particular. The note is
relatively new, and an effort to caution users against potentially unstable
settings.
-Justin
>
> Robin
>
>
> Javier Cerezo wrote:
>> Hello.
>>
>> It looks like you're missing the bonded-interactions parameters.
>>
>> [ bonds ]
>> ; ai aj funct *R0 Kb
>> *1 2 1 * X X*
>> 1 3 1 * X X*
>> 1 4 1 * X X*
>> 1 5 1 * X X*
>> 5 6 1 * X X*
>>
>> (also angles...)
>>
>> Is it implicit somewhere? I don't know if it is automatic and if so,
>> from where the parameters are taken. If it is by using atoms names and
>> the ffbonded.itp from oplsaa, then atom name OA is missing in the itp file.
>>
>> I think that, according to the code (grompp.c), this note may arise if
>> the force constants are zero.
>>
>
> Atom types are interpolated from ffbonded.itp and assigned. If the problem were
> in the bonded parameters, a very different fatal error arises. There is no
> problem here.
>
> -Justin
>
>> Javier
>>
>>
>> El 02/12/10 17:11, Robin C. Underwood escribió:
>>> GMX Users:
>>>
>>> When I run grompp on methanol in water in v. 4.5.3 I get the following Note:
>>>
>>> NOTE 1 [file methanol.top, line 73]:
>>> The bond in molecule-type MET between atoms 5 OA and 6 HO has an
>>> estimated oscillational period of 9.0e-03 ps, which is less than 10 times
>>> the time step of 1.0e-03 ps.
>>> Maybe you forgot to change the constraints mdp option.
>>>
>>> Here is my mdp file:
>>>
>>> ; User Robin
>>> ; Wed Dec.1 2010
>>> ; Input file
>>> ;
>>> title = Yo
>>> cpp = /lib/cpp
>>> integrator = md
>>> dt = 0.001 ; ps !
>>> nsteps = 1100000 ; total 1000 ps=1 ns
>>> nstcomm = 10
>>> ; (x) coordinates, (v) is velocities, (f) is forces
>>> ; This affects "traj.trr"
>>> ; these numbers shouldn't be too small (100,000), takes up disk space
>>> nstxout = 1000
>>> nstvout = 1000
>>> nstfout = 1000
>>> ; Output frequency for energies
>>> nstlog = 100
>>> nstenergy = 100
>>> ; This affects ".xtc" file for movies this should be a fairly small number
>>> nstxtcout = 100
>>> xtc-precision = 1000
>>> ; parameters for neighbors
>>> nstlist = 10
>>> ns_type = grid
>>> rlist = 0.9
>>> ; electrostatics
>>> coulombtype = pme
>>> pme_order = 4
>>> ewald_rtol = 1e-5
>>> ewald_geometry = 3d
>>> epsilon_surface = 0
>>> fourierspacing = 0.1
>>> fourier_nx = 0.0
>>> fourier_ny = 0.0
>>> fourier_nz = 0.0
>>> rcoulomb = 0.9
>>> optimize_fft = yes
>>> Dispcorr = EnerPres
>>> vdwtype = cutoff
>>> rvdw_switch = 0.85
>>> rvdw = 0.9
>>> ; Berendsen temperature coupling is on in two groups
>>> Tcoupl = v_rescale
>>> tc-grps = system
>>> tau_t = 0.1
>>> ref_t = 300
>>> ; Energy monitoring
>>> energygrps = MET SOL
>>> ; Isotropic pressure coupling is now on
>>> Pcoupl = berendsen
>>> Pcoupltype = isotropic
>>> tau_p = 0.5
>>> compressibility = 4.5e-5
>>> ref_p = 1.0
>>> ; Generate velocites is off at 300 K.
>>> gen_vel = no
>>> gen_temp = 300.0
>>> gen_seed = 173529
>>>
>>>
>>> Here is my top file:
>>>
>>> ;
>>> ;
>>> ; Include forcefield parameters
>>> #include "ffoplsaa.itp"
>>>
>>> ;
>>> ; Methanol, Jorgensen et al. JACS 118 pp. 11225 (1996)
>>> ;
>>> [ moleculetype ]
>>> ; name nrexcl
>>> MET 3
>>>
>>> [ atoms ]
>>> ; nr type resnr residu atom cgnr charge mass
>>> 1 opls_157 1 MET C 1 0.145
>>> 2 opls_156 1 MET H 1 0.04
>>> 3 opls_156 1 MET H 1 0.04
>>> 4 opls_156 1 MET H 1 0.04
>>> 5 opls_154 1 MET OA 1 -0.683
>>> 6 opls_155 1 MET HO 1 0.418
>>>
>>> [ bonds ]
>>> ; ai aj funct c0 c1
>>> 1 2 1
>>> 1 3 1
>>> 1 4 1
>>> 1 5 1
>>> 5 6 1
>>>
>>> [ pairs ]
>>> ; i j funct
>>> 2 6
>>> 3 6
>>> 4 6
>>>
>>> [ angles ]
>>> ; ai aj ak funct c0 c1
>>> ; H3
>>> 2 1 5 1
>>> 3 1 5 1
>>> 4 1 5 1
>>> 4 1 3 1
>>> 4 1 2 1
>>>
>>>
>>> [ system ]
>>> ; Name
>>> MET in water
>>>
>>> [ molecules ]
>>> ; Compound #mols
>>> MET 1
>>> SOL 503
>>>
>>>
>>> Do I need to add some sort of constraint on my methanol molecule?
>>>
>>> Thanks,
>>> Robin
>>>
>>>
>>>
>> --
>> Javier CEREZO BASTIDA
>> Estudiante de Doctorado
>> ---------------------
>> Dpto. Química-Física
>> Universidad de Murcia
>> 30100 MURCIA (España)
>> Tlf.(+34)868887434
>>
>
> --
> ==============================
>
> ==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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