[gmx-users] Normal mode analysis
jair at iq.ufrj.br
Fri Dec 9 19:30:43 CET 2005
On Friday 09 December 2005 16:16, David van der Spoel wrote:
> jjvc wrote:
> > 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 method.
> > 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 lbfgs15.edr
> > 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?
> Sorry to ask for the obvious, but are you sure you used the right
> coordinates? Try using the output trr from the minimization.
> > Thanks
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Thanks for your answer.
In principle I used the correct trajectory from the minimization.
But I have a doubt: The minimization were done in various steps by changing
the emtol ant emstep parameters. But after each step (mdrun execution) I
didn't use the .trr file for the new grompp execution. Maybe the error is in
Anyway I will redo everything and I'll double check these things
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