[gmx-users] Check for bad contacts and/or reduce the timestep

[Justin A. Lemkul]

nishap.patel at utoronto.ca wrote:
> Hi,
> 
>  I am trying to run a simulation with 1360 Tip4p water molecules and one 
> methane molecule (Box size: 35.500 35.3371 35.500 and Total 5541 atoms) 
> but I am getting the error:
> 
> t = 0.000 ps: Water molecule starting at atom 5433 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> 

Have you done sufficient energy minimization?  General information can be found 
within the wiki pages of the Gromacs site, i.e.:

http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

-Justin

> Here is my grompp. file :
> 
> 
> ; RUN CONTROL PARAMETERS =
> integrator               = md
> ; start time and timestep in ps =
> tinit                    = 0.0
> dt                       = 0.002
> nsteps                   = 25000
> ; number of steps for center of mass motion removal =
> nstcomm                  = 1
> 
>  ENERGY MINIMIZATION OPTIONS
> emtol                    = 10000
> emstep                   = 0.01
> 
> ; OUTPUT CONTROL OPTIONS =
> ; Output frequency for coords (x), velocities (v) and forces (f) =
> nstxout                  = 1000
> nstvout                  = 1000
> nstfout                  = 0
> ; Output frequency for energies to log file and energy file =
> nstlog                   = 0
> nstenergy                = 100
> ; Output frequency and precision for xtc file =
> nstxtcout                = 100
> xtc_precision            = 1000
> ; This selects the subset of atoms for the xtc file. =
> ; Only the first group gets written out, it does not make sense =
> ; to have multiple groups. By default all atoms will be written =
> xtc_grps                 =
> ; Selection of energy groups =
> energygrps               = CH4 SOL
> 
> 
> ; NEIGHBORSEARCHING PARAMETERS =
> ; nblist update frequency =
> nstlist                  = 1.0
> ; ns algorithm (simple or grid) =
> ns_type                  = grid
> ; nblist cut-off         =
> rlist                    = 1.0
> 
> ; OPTIONS FOR ELECTROSTATICS AND VDW =
> ; Method for doing electrostatics =
> coulomb_type             = pme
> rcoulomb_switch          = 0
> rcoulomb                 = 1.0
> ; Dielectric constant (DC) for cut-off or DC of reaction field =
> epsilon_r                = 1.0
> epsilon_rf               = 0
> ; Method for doing Van der Waals =
> vdw_type                 = Cut-off
> ; cut-off lengths        =
> rvdw_switch              = 0
> rvdw                     = 1.0
> dispcorr                 = enerpres
> 
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
> ; Temperature coupling   =
> tcoupl                   = v-rescale
> ; Groups to couple separately =
> tc-grps                  = system
> ; Time constant (ps) and reference temperature (K) =
> tau_t                    = 0.1
> ref_t                    = 300
> 
> ; Pressure coupling      =
> Pcoupl                   = Berendsen
> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
> tau_p                    = 1.0
> compressibility          = 4.6e-5
> ref_p                    = 1
> 
> 
> ; GENERATE VELOCITIES FOR STARTUP RUN =
> gen_vel                  = yes
> gen_temp                 = 300
> gen_seed                 = 171533
> 
> I am new to this, so any inputs would be appreciated.
> 
> Thanks
> 
> Nisha
> 

-- 
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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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