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

[Javier Cerezo]

El 02/12/10 19:02, Justin A. Lemkul escribió:
>
>
> 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.
I see it now, the stimated frequency fits with the force constat in 
ffbonded.itp and masses in ffnonbonded.itp.
Thanks

(That's a nice new check in grompp, by the way.)
>
> -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
>>
>

-- 
Javier CEREZO BASTIDA
Estudiante de Doctorado
---------------------
Dpto. Química-Física
Universidad de Murcia
30100 MURCIA (España)
Tlf.(+34)868887434