[gmx-users] Potential Energy = -nan

[Justin A. Lemkul]

shikha agarwal wrote:
> 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!
> 

You've proven that the problem is not platform-specific, but you've provided 
none of the other details I requested before.  Something is wrong with either 
the way you're building the system or constructed the topology.  If you want 
free help, you have to make it easy to help you.  So far, you haven't.  Please 
consult my previous message and provide all the details I requested.  Otherwise, 
you're unlikely to get anyone to help you.

-Justin

> 
> 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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