When I do the energy minimization of my system contain a protein, an ATP and water molecules using mdrun, it stopped at 15 steps, and return following messeges:
Steepest Descents:
Tolerance (Fmax) = 1.00000e+00
Number of steps = 2000
Step= 0, Dmax= 1.0e-02 nm, Epot= -3.24259e+05 Fmax= 3.22275e+04, atom= 1264
Step= 14, Dmax= 1.2e-06 nm, Epot= nan Fmax= 2.96890e+04, atom= 1262
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1
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 15 steps,
but did not reach the requested Fmax < 1.
Potential Energy = -3.2425944e+05
Maximum force = 3.2227543e+04 on atom 1264
Norm of force = nan
what's wrong with it?
p.s. My .mdp file is:
integrator = steep ;minimization method
emtol = 1.0 ; stop minimization when max force < 1.0 KJ/mol
nsteps = 2000 ; max step number
nstenergy = 10 ;n step to write energy
nstxtcout = 10 ;n step to write coordinates file
nstlist = 1 ;the step to update the neighbour step list
ns_type = simple; the method to det ermine neighbour list
rlist = 1.0 ;cutoff for make neighbour list
coulombtype = cutoff ;cutoff for electrostatic force distance
rcoulomb = 1.0 ;long range cutoff for elect.
rvdw = 1.0 ; long range cutoff for vdw
constraints = none ;no constraint
pbc = no ; no periode boundary conditions
Best wishes!
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