[gmx-users] A question about "blowing up"

[sujith ks]

Hello Justin,

  I performed energy minimization , the way you performed for the free
energy calculation for the methane-water system in the tutorial. In the
first step steepest descent was used followed by l-bfgs. The emtol (force)
was set to 10 kj/mol/nm.

The final results can be summerized as:

Low-Memory BFGS Minimizer converged to Fmax < 10 in 7929 steps
Potential Energy  = -9.4460383e+04
Maximum force     =  7.4954224e+00 on atom 1760
Norm of force     =  5.8917433e-01

The potential vs time graph looks good (converged).

 The .mdp is as follows:

; Run control
integrator               = l-bfgs
nsteps                   = 100000
define                    = -DFLEXIBLE
; EM criteria and other stuff
emtol                      = 10
emstep                   = 0.01
niter                        = 20
nbfgscorr                 = 10
; Output control
nstlog                      = 1
nstenergy                = 1
; Neighborsearching and short-range nonbonded interactions
nstlist                     = 1
ns_type                  = grid
pbc                        = xyz
rlist                        = 0.9
; Electrostatics
coulombtype              = pme
rcoulomb                   = 0.9
; van der Waals
vdw-type                 = Cut-off
rvdw                       = 1.4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                   = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing            = 0.12
; EWALD/PME/PPPM parameters
pme_order                 = 6
ewald_rtol                 = 1e-06
epsilon_surface          = 0
optimize_fft               = no
; Temperature and pressure coupling are off during EM
tcoupl                    = no
pcoupl                   = no
; Generate velocities to start
gen_vel                  = no
; options for bonds
constraints              = none
; Type of constraint algorithm
constraint-algorithm     = lincs
; Do not constrain the starting configuration
continuation             = no
; Highest order in the expansion of the constraint coupling matrix
lincs-order               = 12
~                                                                                                                                                                                   
Thanks,

Sujith.                                     
~                                                                                                                                                                                 


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