[gmx-users] problem in energy minimization

neelam wafa neelam.wafa at gmail.com
Tue Jul 17 15:12:17 CEST 2018


Dear gromacs users, I am running md simmulation of a protein with a ligand.
i have already done it with the same protein and a different ligand. Now
when i run em md run i get following result.

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 150 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -9.3659806e+05
Maximum force     =  1.0269271e+04 on atom 4399
Norm of force     =  9.8929054e+01

NOTE: 10 % of the run time was spent in pair search,
      you might want to increase nstlist (this has no effect on accuracy)
 please guide me is it reliable to proceede for simmulation. or there is
something wrong. Is it a sign of system instability?

looking forward for your cooperation.


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