[gmx-users] Grompp note

[Nilesh Dhumal]

Could you tell how can I get rid of following warning?


WARNING 1 [file test.top, line 263]:
  The bond in molecule-type BMI between atoms 10 C10 and 23 H23 has an
  estimated oscillational period of 1.2e-03 ps, which is less than 5 times
  the time step of 1.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.



>
> On 10/31/13 10:30 AM, Nilesh Dhumal wrote:
>> Hello,
>>
>> I am running a equilibration simulation for ionic liquids  at 400 K.
>>
>> I am getting following note.
>>
>>   The sum of the two largest charge group radii (0.213127) is larger
>> than
>>    rlist (1.000000) - rvdw (0.900000)
>>
>> Could you tell what is the problem?  I am using Gromacs VERSION 4.5.5 .
>>
>
> http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
>
> Also see the numerous discussions on this topic in the list archive.
>
> -Justin
>
>>
>> I used the following mdp file.
>>
>> ; RUN CONTROL PARAMETERS =
>> integrator               = sd
>> ; start time and timestep in ps =
>> tinit                    = 0
>> dt                       = 0.001
>> nsteps                   = 200000
>> ; number of steps for center of mass motion removal =
>> nstcomm                  = 100
>> ; OUTPUT CONTROL OPTIONS =
>> ; Output frequency for coords (x), velocities (v) and forces (f) =
>> nstxout                  = 0
>> nstvout                  = 0
>> nstfout                  = 0
>> ; Output frequency for energies to log file and energy file =
>> nstlog                   = 5000
>> nstenergy                = 1000
>> ; Output frequency and precision for xtc file =
>> nstxtcout                = 5000
>> xtc-precision            = 1000
>> ; NEIGHBORSEARCHING PARAMETERS =
>> ; nblist update frequency =
>> nstlist                  = 10
>> ; ns algorithm (simple or grid) =
>> ns_type                  = grid
>> ;OPTIONS FOR TEMPERATURE COUPLING
>> tc_grps                  = system
>> tau_t                    = 0.1
>> ref_t                    = 400
>> ;OPTIONS FOR PRESSURE COUPLING
>> Pcoupl                   = berendsen
>> tau_p                    = 0.5
>> compressibility          = 4.5e-05
>> ref_p                    = 1.0
>> ; OPTIONS FOR BONDS     =
>> constraints              = hbonds
>> ; Type of constraint algorithm =
>> constraint-algorithm     = Lincs
>> ; Do not constrain the start configuration =
>> unconstrained-start      = no
>> ; Relative tolerance of shake =
>> shake-tol                = 0.0001
>> ; Highest order in the expansion of the constraint coupling matrix =
>> lincs-order              = 12
>> ; Lincs will write a warning to the stderr if in one step a bond =
>> ; rotates over more degrees than =
>> lincs-warnangle          = 30
>>
>> ; Periodic boundary conditions: xyz or none =
>> pbc                      = xyz
>> ; nblist cut-off         =
>> rlist                    = 1.0
>> domain-decomposition     = no
>> ; OPTIONS FOR ELECTROSTATICS AND VDW =
>> ; Method for doing electrostatics =
>> coulombtype              = pme
>> ;rcoulomb-switch          = 0
>> rcoulomb                 = 1.0
>> ; Dielectric constant (DC) for cut-off or DC of reaction field =
>> epsilon-r                = 1
>> ; Method for doing Van der Waals =
>> vdw-type                 = switch
>> ; cut-off lengths        =
>> rvdw-switch              = 0.8
>> rvdw                     = 0.9
>> ; Apply long range dispersion corrections for Energy and Pressure =
>> DispCorr                  = EnerPres
>> ; Spacing for the PME/PPPM FFT grid =
>> fourierspacing           = 0.1
>> ; FFT grid size, when a value is 0 fourierspacing will be used =
>> fourier_nx               = 0
>> fourier_ny               = 0
>> fourier_nz               = 0
>> ; EWALD/PME/PPPM parameters =
>> pme_order                = 6
>> ewald_rtol               = 1e-06
>> epsilon_surface          = 0
>> optimize_fft             = no
>> ; Free energy control stuff
>> free_energy              = no
>>
>>
>> Nilesh
>>
>>
>>
>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
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