[gmx-users] Grompp note

[Justin Lemkul]

On 10/31/13 11:40 AM, Nilesh Dhumal wrote:
> 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.
>

The relationship between high-frequency vibrations and the chosen timestep is a 
fundamental point in MD simulations.  Any textbook covers it.  There are even a 
few hints in the Gromacs manual.

-Justin

>
>
>>
>> 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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>
>

-- 
==================================================

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

==================================================