[gmx-users] Potential Energy = -nan

[Justin A. Lemkul]

shikha agarwal wrote:
> hi
> 
> 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.

-Justin

> 
> help me !
> 
> with regards:
> shikha
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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