[gmx-users] Energy minimization
shima_arasteh2001 at yahoo.com
Sat Sep 29 09:19:10 CEST 2012
My system contains lipids, protein and water.
I want to energy minimize it, so ran grompp:
# grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr
# mdrun -v -deffnm em
The output is:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= 518
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)
writing lowest energy coordinates.
Back Off! I just backed up em.gro to ./#em.gro.3#
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 2.3000388e+17
Maximum force = inf on atom 518
Norm of force = inf
It seems that atome 518 has an infinite energy. So I tried to apply the suggestion of turning off the constraints in em.mdp. To do so, I added "constraints=none" to mdp file, But it doesn't make different.
Any suggestion please? I don't know how to solve this problem. Please help me.
Thanks in advance.
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