[gmx-users] problem in energy minimization
dallas.warren at monash.edu
Wed Jul 18 01:57:01 CEST 2018
On Tue, 17 Jul. 2018, 11:12 pm neelam wafa, <neelam.wafa at gmail.com> wrote:
> 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
> It stopped because the algorithm tried to make a new step whose size was
> 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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