On 7/26/12 8:30 AM, tarak karmakar wrote:
Dear All,
While running minimization I imposed the the condition for the
minimization as to be converged only at Fmax < 10 . But I got the
following
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)
Steepest Descents converged to machine precision in 15318 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -3.3397742e+06
Maximum force = 9.8232233e+02 on atom 6057
Norm of force = 3.6321018e+00
Then according to the above instruction I increased the stepsize up to
0.5 [ I didn't use any constraint during minimization] but got the
same. So do I need to increase the stepsize more or is there other
procedure to get to the desired convergence criteria ?
The minimization .mdp file is as follows
Have you consulted the following?
http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision
It may simply not be possible to energy minimize the system further without
using double precision or a better EM algorithm. Steepest descents converges
very quickly but the results can often be improved by additional rounds of CG or
L-BGFS minimization. For most purposes, one does not require such a low maximum
force, but if you need Fmax < 10, then you likely need a significantly more
robust protocol.
-Justin
; 7.3.2 Preprocessing
;define = -DFLEXIBLE ; defines to pass to the preprocessor
; 7.3.3 Run Control
integrator = steep ; steepest descents energy minimization
nsteps = 100000 ; maximum number of steps to integrate
; 7.3.5 Energy Minimization
emtol = 10 ; [kJ/mol/nm] minimization is
converged when max force is < emtol
emstep = 0.01 ; [nm] initial step-size
nstcgsteep = 10 ; freq of performing one
steepest descent step
; 7.3.8 Output Control
nstxout = 500 ; [steps] freq to write
coordinates to trajectory
nstvout = 500 ; [steps] freq to write
velocities to trajectory
nstfout = 500 ; [steps] freq to write forces
to trajectory
nstlog = 100 ; [steps] freq to write
energies to log file
nstenergy = 100 ; [steps] freq to write
energies to energy file
energygrps = System ; group(s) to write to energy file
; 7.3.9 Neighbor Searching
nstlist = 1 ; [steps] freq to update neighbor list
ns_type = grid ; method of updating neighbor list
pbc = xyz ; periodic boundary conditions
in all directions
rlist = 0.8 ; [nm] cut-off distance for
the short-range neighbor list
; 7.3.10 Electrostatics
coulombtype = PME ; Particle-Mesh Ewald electrostatics
rcoulomb = 0.8 ; [nm] distance for Coulomb cut-off
; 7.3.11 VdW
vdwtype = cut-off ; twin-range cut-off with
rlist where rvdw >= rlist
rvdw = 0.8 ; [nm] distance for LJ cut-off
DispCorr = Ener ; apply long range dispersion
corrections for energy
; 7.3.13 Ewald
fourierspacing = 0.12 ; [nm] grid spacing for FFT
grid when using PME
pme_order = 4 ; interpolation order for PME, 4 = cubic
ewald_rtol = 1e-5 ; relative strength of
Ewald-shifted potential at rcoulomb
Thanks,
Tarak
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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