[gmx-users] Grompp note
jalemkul at vt.edu
Thu Oct 31 17:22:59 CET 2013
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.
>> On 10/31/13 10:30 AM, Nilesh Dhumal wrote:
>>> 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
>>> rlist (1.000000) - rvdw (0.900000)
>>> Could you tell what is the problem? I am using Gromacs VERSION 4.5.5 .
>> Also see the numerous discussions on this topic in the list archive.
>>> 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
>> 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
>> gmx-users mailing list gmx-users at gromacs.org
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Justin A. Lemkul, Ph.D.
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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