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

[Javier Cerezo]

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.

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

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