[gmx-users] Potential Energy = -nan

[shikha agarwal]

hi
>  I m using gromacs4.5.3 . hardware 1GB ram 320 hard disk .
when i skiped scaling by factor 0.95 then , after EM step I m getting same
potential energy nan result.








> i m doing simulation membrane protein
> while scaling  down the lipids by a factor of 0.95 then performing EM
>
> Steepest Descents converged to Fmax < 10 in 18 steps
> Potential Energy  = -nan
> Maximum force     =  4.7791553e+02 on atom 5440
> Norm of force     =  -nan
>
>
>
> ; 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          = 0.1          ; 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)
> define = -DSTRONG_POSRES
>
>
> earlier when i was using
>
> ; 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        = 1000.0      ; Stop minimization when the maximum force <
> 1000.0 kJ/mol/nm
> emstep          = 0.01          ; Energy step size
> nsteps        = 50000          ; Maximum number of (minimization) steps
> to perform
>
> ; Parameters describing how to find the neighbors of each atom and how
> to calculate the interactions
> nstlist        = 1        ; 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    = PME        ; 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)
> define = -DFLEXIBLE
>
>
> then problem was same
>

Which version of Gromacs?  On what hardware?  I discovered a
platform-specific
bug that looked a lot like this, but I hesitate to suggest that until I know
more.

In all likelihood, you simply have unresolvable atomic overlap (i.e., you're
packing too much) such that energy minimization cannot complete, since nan =
"not a number," or something is infinitely large or small.
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