[gmx-users] Potential Energy = -nan

[shikha agarwal]

hi,

I tried on other system , 4GB ram , core i3 ,64bit processor


; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator    = steep        ; Algorithm (steep = steepest descent
minimization)
emtol        = 10.0      ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep          = 0.01          ; Energy step size
nsteps        = 25000          ; Maximum number of (minimization) steps to
perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist        = 10        ; Frequency to update the neighbor list and long
range forces
ns_type        = grid        ; Method to determine neighbor list (simple,
grid)
rlist        = 1.2        ; Cut-off for making neighbor list (short range
forces)
coulombtype    = Shift        ; Treatment of long range electrostatic
interactions
rcoulomb    = 1.2        ; Short-range electrostatic cut-off
rvdw        = 1.2        ; Short-range Van der Waals cut-off
pbc        = xyz         ; Periodic Boundary Conditions (yes/no)
nstxout         =   1




result''''''''

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+01
   Number of steps    =        25000
Step=   14, Dmax= 1.2e-06 nm, Epot=         -nan Fmax= 3.56233e+07, atom=
2455
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.

writing lowest energy coordinates.

Back Off! I just backed up after_em2.gro to ./#after_em2.gro.1#

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 10.
Potential Energy  =           -nan
Maximum force     =  3.5637456e+07 on atom 2455
Norm of force     =           -nan


help me!


shikha
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