[gmx-users] problem normal mode analysis

Ran Friedman r.friedman at bioc.uzh.ch
Fri Feb 12 16:21:33 CET 2010

I guess posting the whole set of commands you used and mdp file for NMA
can help.

sarbani chattopadhyay wrote:
> hi,
> I want to do a normal mode analysis on a small peptide.
> I had complied gromacs in double precision and energy minimized the
> structure in vacuum,
> using steepest descent followed by conjugate gradient method. the log
> file of conjugate
> gradient method reads
> Polak-Ribiere Conjugate Gradients converged to Fmax < 0.0001 in 1023 steps
> Potential Energy = -1.95899271351756e+02
> Maximum force = 9.50250289517625e-05 on atom 48
> Norm of force = 3.82317661305055e-05
> but when i try to run mdrun_d ( for normal mode analysis) , it shows
> Maximum force: 2.05241e+02
> Maximum force probably not small enough to ensure that you are in an
> energy well. Be aware that negative eigenvalues may occur when the
> resulting matrix is diagonalized
> I had made grompp_d read the trajectory file of "cg energy
> minimization" by using the -t
> flag.
> where have i gone wrong?
> Any suggestion will be of great help.
> Thanks in advance.
> Sarbani Chattopadhyay
> <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle?>

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