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g_nmeig_d
Langue: en
Version: 261720 (debian - 07/07/09)
Section: 1 (Commandes utilisateur)
NAME
g_nmeig - diagonalizes the HessianSYNOPSIS
g_nmeig -f hessian.mtx -s topol.tpr -of eigenfreq.xvg -ol eigenval.xvg -v eigenvec.trr -[no]h -nice int -[no]xvgr -[no]m -first int -last intDESCRIPTION
g_nmeig calculates the eigenvectors/values of a (Hessian) matrix, which can be calculated with mdrun The eigenvectors are written to a trajectory file ( -v ). The structure is written first with t=0. The eigenvectors are written as frames with the eigenvector number as timestamp. The eigenvectors can be analyzed with g_anaeig An ensemble of structures can be generated from the eigenvectors withg_nmens . When mass weighting is used, the generated eigenvectors will be scaled back to plain cartesian coordinates before generating the output - in this case they will no longer be exactly orthogonal in the standard cartesian norm (But in the mass weighted norm they would be).
FILES
-f hessian.mtx InputHessian matrix
-s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb xml
-of eigenfreq.xvg Output
xvgr/xmgr file
-ol eigenval.xvg Output
xvgr/xmgr file
-v eigenvec.trr Output
Full precision trajectory: trr trj
OTHER OPTIONS
-[no]h noPrint help info and quit
-nice int 19
Set the nicelevel
-[no]xvgr yes
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-[no]m yes
Divide elements of Hessian by product of sqrt(mass) of involved atoms prior to diagonalization. This should be used for 'Normal Modes' analysis
-first int 1
First eigenvector to write away
-last int 50
Last eigenvector to write away
SEE ALSO
gromacs(7)More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre