[gmx-users] mdp file problem

[Justin A. Lemkul]

madhumita das wrote:
> 
> Hi GROMACS users,
> 
>     i am in the midst of simulating  a protein in water.  I have 
> modified  a residue  in my  pdb file at position  182,  using amber and 
> then acpype.py.  But  after running  the energy minimization step,using  
> em.mdp file  generated from acpype , following error comes.
> 
> Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+03
>    Number of steps    =         5000
> Step=   17, Dmax= 1.5e-06 nm, Epot=  9.89827e+17 Fmax=         inf, 
> atom= 2700
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1000
> 
> Double precision normally gives you higher accuracy.
> 
> writing lowest energy coordinates.
> 
> Steepest Descents converged to machine precision in 18 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  =  9.8982703e+17
> Maximum force     =            inf on atom 2700
> Norm of force     =  1.7474532e+19

An infinite force suggests severe atomic overlap.  Check the starting structure, 
paying close attention to atom 2700 and its surrounding environment.

-Justin

-- 
========================================

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

========================================