On 9/29/12 3:19 AM, Shima Arasteh wrote:
Dear all,
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
and then:
# mdrun -v -deffnm em
The output is:
Steepest Descents:
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.
Atom 518 is overlapping with something nearby. You will have to visualize the
system to identify the source of the problem.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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