[gmx-users] Minimization problem
mark.j.abraham at gmail.com
Tue Jan 9 23:52:15 CET 2018
You're also using tabulated VDW interactions, so I'd start by looking at
that. What steps have you taken to ensure that each of your topologies
works, e.g. on their own in vacuum?
On Tue, Jan 9, 2018 at 11:46 PM Neda Rafiee <nerafiee at ipm.ir> wrote:
> Dear Users,
> I have a problem in energy minimization step. Actually I have some groups
> of atoms that are freezed and also a chain of protein in water. I want the
> following items:
> constraints = none
> integrator = steep
> emstep = 0.0001
> emtol = 500.0
> nsteps = 500000
> ; Neighbor list and pbc's ------------------------------------------
> cutoff-scheme = group
> nstlist = 1 ; default is 10 -- try more frequent
> ns_type = grid ; simple (for no pbc) or grid
> pbc = xyz ; CHANGE
> periodic_molecules = no
> ; Interaction parameters -------------------------------------------
> rlist = 1
> rlistlong = 1
> rcoulomb = 1
> coulombtype = PME
> epsilon_r = 1
> vdwtype = user; cut-off
> rvdw = 1
> but after just 6000 steps it gives me this error:
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 500 (which may not be possible for your system).
> 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.
> 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 53429 steps,
> but did not reach the requested Fmax < 500.
> Potential Energy = 2.46705107676305e+14
> Maximum force = 9.69602643026733e+08 on atom 9415
> Norm of force = 1.70746371816015e+07
> Would you please help me understand where the problem is ?!
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