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.
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
========================================
--
Robin C. Underwood
Chemistry Department
560 Oval Drive
West Lafayette, IN 47907
--
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