[gmx-users] Normal mode analysis
David van der Spoel
spoel at xray.bmc.uu.se
Fri Dec 9 19:16:24 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?
Sorry to ask for the obvious, but are you sure you used the right
coordinates? Try using the output trr from the minimization.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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