[gmx-users] Normal mode analysis

[David van der Spoel]

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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-- 
David.
________________________________________________________________________
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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