[gmx-users] Check for bad contacts and/or reduce the timestep
nishap.patel at utoronto.ca
nishap.patel at utoronto.ca
Mon Dec 14 20:07:05 CET 2009
----- Forwarded message from nishap.patel at utoronto.ca -----
Date: Mon, 14 Dec 2009 14:06:30 -0500
From: nishap.patel at utoronto.ca
Reply-To: nishap.patel at utoronto.ca
Subject: Re: [gmx-users] Check for bad contacts and/or reduce the timestep
To: "Justin A. Lemkul" <jalemkul at vt.edu>
I tried to run minimization step and I got the following error:
Steepest Descents:
Tolerance (Fmax) = 1.00000e+01
Number of steps = 25000
Step= 1, Dmax= 1.0e-02 nm, Epot= 1.57470e+09 Fmax= 2.12566e+11, atom= 4973
Step= 2, Dmax= 1.2e-02 nm, Epot= 2.42785e+08 Fmax= 2.02821e+10, atom= 4985
Step= 3, Dmax= 1.4e-02 nm, Epot= 6.83525e+07 Fmax= 2.24629e+09, atom= 4973
Step= 4, Dmax= 1.7e-02 nm, Epot= 1.36192e+07 Fmax= 2.34481e+08, atom= 4985
Step= 5, Dmax= 2.1e-02 nm, Epot= 3.37948e+06 Fmax= 2.50839e+07, atom= 4973
Step= 6, Dmax= 2.5e-02 nm, Epot= 9.58580e+05 Fmax= 2.79175e+06, atom= 1321
Step= 7, Dmax= 3.0e-02 nm, Epot= 2.98861e+05 Fmax= 3.83032e+06, atom= 4973
Step= 8, Dmax= 3.6e-02 nm, Epot= 2.15478e+05 Fmax= 5.79850e+05, atom= 4973
Step= 9, Dmax= 4.3e-02 nm, Epot= 7.16581e+04 Fmax= 1.12895e+06, atom= 4973
Step= 10, Dmax= 5.2e-02 nm, Epot= 4.39860e+04 Fmax= 7.57820e+04, atom= 101
t = 0.022 ps: Water molecule starting at atom 101 can not be settled.
Check for bad contacts and/or reduce the timestep.
Back Off! I just backed up step11b.pdb to ./#step11b.pdb.6#
Back Off! I just backed up step11c.pdb to ./#step11c.pdb.6#
Wrote pdb files with previous and current coordinates
Step= 11, Dmax= 6.2e-02 nm, Epot= -1.94430e+04 Fmax= 7.60249e+04, atom= 102
Step= 12, Dmax= 7.4e-02 nm, Epot= -2.29926e+04 Fmax= 3.21409e+05, atom= 4917
t = 0.026 ps: Water molecule starting at atom 4917 can not be settled.
Check for bad contacts and/or reduce the timestep.
Back Off! I just backed up step13b.pdb to ./#step13b.pdb.6#
Back Off! I just backed up step13c.pdb to ./#step13c.pdb.6#
Wrote pdb files with previous and current coordinates
Step= 14, Dmax= 4.5e-02 nm, Epot= -2.80812e+04 Fmax= 1.42056e+04, atom= 9577
Step= 15, Dmax= 5.3e-02 nm, Epot= -3.28009e+04 Fmax= 1.37135e+05, atom= 4893
t = 0.032 ps: Water molecule starting at atom 4893 can not be settled.
Check for bad contacts and/or reduce the timestep.
Back Off! I just backed up step16b.pdb to ./#step16b.pdb.6#
Back Off! I just backed up step16c.pdb to ./#step16c.pdb.6#
Wrote pdb files with previous and current coordinates
Step= 16, Dmax= 6.4e-02 nm, Epot= -3.72070e+04 Fmax= 2.01112e+04, atom= 1217
t = 0.034 ps: Water molecule starting at atom 4917 can not be settled.
Check for bad contacts and/or reduce the timestep.
Back Off! I just backed up step17b.pdb to ./#step17b.pdb.2#
Back Off! I just backed up step17c.pdb to ./#step17c.pdb.2#
Wrote pdb files with previous and current coordinates
Step= 33, Dmax= 1.2e-06 nm, Epot= -1.10597e+04 Fmax= 1.29469e+06, atom= 4893
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 34 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -3.7206969e+04
Maximum force = 2.0111207e+04 on atom 1217
Norm of force = 6.9283209e+02
I don't understand constraints I need to turn off, since I haven't
mentioned any in my grompp file.
-Nisha
>
>
> 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
>>
>
> --
> ========================================
>
> 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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