[gmx-users] Re: Note on oscillation period / time step

[Robin C. Underwood]

    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