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

[Naga Rajesh Tummala]

Robin,

Easiest way to get it running, with the flexible bond between O and H in
methane would be to decrease the time step. I would start with half a femto
second time step and see what happens.

All the best
Rajesh

On Thu, Dec 2, 2010 at 10:11 AM, Robin C. Underwood <rcunderw at purdue.edu>wrote:

> 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
>
>
> --
> Robin C. Underwood
> Chemistry Department
> 560 Oval Drive
> West Lafayette, IN 47907
> --
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-- 
Naga Rajesh Tummala, PhD
School of Chemical, Biological, and Materials Engineering
University of Oklahoma
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