[gmx-users] Cannot minimiza - vdwradii.dat ???
s.neumann08 at gmail.com
Thu Nov 15 14:41:04 CET 2012
Dear Gmx Users,
I am trying to run simulations of protein and FE(2+) atoms. I placed
them randomly around the protein, solvated the system and tried to
minimize. After grompp, I tried mdrun:
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.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
Steepest Descents converged to machine precision in 62 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = -7.2573600e+05
Maximum force = 5.7863950e+05 on atom 756
Norm of force = 3.5862925e+03
I tried different stepsizes, constarint = none etc but never converged
to requested Fmax < 1000
When I try NVT:
2 particles communicated to PME node 0 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
This usually means that your system is not well equilibrated.
So the problem is with minimization.
My question: Can it be the problem of not specified vdwradius of my
FE(2+) in vdwradii.dat ? I mean, can ater molecules overlap with
Ferrous and thus minimization does not converge?
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