[gmx-users] Energy minimization

Shima Arasteh shima_arasteh2001 at yahoo.com
Sat Sep 29 09:19:10 CEST 2012

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.

Thanks in advance.


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