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
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