----- Forwarded message from [email protected] -----
Date: Mon, 14 Dec 2009 14:06:30 -0500
From: [email protected]
Reply-To: [email protected]
Subject: Re: [gmx-users] Check for bad contacts and/or reduce the timestep
To: "Justin A. Lemkul" <[email protected]>
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
[email protected] 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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