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

[Justin A. Lemkul]

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

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