[gmx-users] Normal mode analysis

jjvc jair at iq.ufrj.br
Fri Dec 9 19:05:22 CET 2005

I'm tryng to do a normal mode analysis with gromacs
I performed the minimization of a protein structure in vacuo using the l-bfgs 
After the minimizaton the results obtained were:

Low-Memory BFGS Minimizer converged to machine precision in 24550 steps,
but did not reach the requested Fmax < 1e-08. 
Potential Energy  = -4.09184275152338e+03 
Maximum force   =  1.66412131872925e-07 on atom 855 
Norm of force      =  8.31243056797603e-09

Then I prepared an .mdp file with just one line

integrator = nm

I run: 
grompp_d -f hess.mdp -c lbfgs15.g96 -p prot.top -o hess.tpr -t lbfgs15.trr -e 

and then:
mdrun_d -v -s hess.tpr -o -c hess.g96 -e hess.edr -g hess.log -mtx hess.mtx

A message of the program appears saying:

Maximum force: 1.36197e+03
Maximum force probably not small enough to ensure that you are in a 
energy well. Be aware that negative eigenvalues may occur when the
resulting matrix is diagonalized.

Ins't the maximum force 1.66412131872925e-07 as show above ?
Am I doing something wrong?


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