[gmx-users] mdp file problem

madhumita das madhumita.bioinfo at gmail.com
Tue Nov 8 12:33:41 CET 2011

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=
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
 The mdp file is attached.

                                   Please help.

Madhumita Das
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