Merged in g_nmtraj manpage from release-3-3-patches

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+.TH g_nmtraj 1 "Tue 6 Sep 2005"
+.SH NAME
+g_nmtraj
+.B VERSION 3.3_beta_20050823
+.SH SYNOPSIS
+\f3g_nmtraj\fP
+.BI "-s" " topol.tpr "
+.BI "-v" " eigenvec.trr "
+.BI "-o" " nmtraj.xtc "
+.BI "-[no]h" ""
+.BI "-nice" " int "
+.BI "-eignr" " int "
+.BI "-temp" " real "
+.BI "-amplitude" " real "
+.BI "-nframes" " int "
+.SH DESCRIPTION
+
+.B g_nmtraj
+generates an virtual trajectory from an eigenvector, 
+corresponding to a harmonic cartesian oscillation around the average 
+structure. The eigenvectors should normally be mass-weighted, but you can 
+use non-weighted eigenvectors to generate orthogonal motions. 
+The output frames are written as a trajectory file covering an entire period, and 
+the first frame is the average structure. If you write the trajectory in (or convert to) 
+PDB format you can view it directly in PyMol and also render a photorealistic movie. 
+Motion amplitudes are calculated from the eigenvalues and a preset temperature, 
+assuming equipartition of the energy over all modes. To make the motion clearly visible 
+in PyMol you might want to amplify it by setting an unrealistic high temperature. 
+However, be aware that both the linear cartesian displacements and mass weighting will 
+lead to serious structure deformation for high amplitudes - this is is simply a limitation 
+of the cartesian normal mode model. By default the selected eigenvector is set to 7, since 
+ the first six normal modes are the translational and rotational degrees of freedom.
+.SH FILES
+.BI "-s" " topol.tpr" 
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml 
+
+.BI "-v" " eigenvec.trr" 
+.B Input
+ Full precision trajectory: trr trj 
+
+.BI "-o" " nmtraj.xtc" 
+.B Output
+ Generic trajectory: xtc trr trj gro g96 pdb 
+
+.SH OTHER OPTIONS
+.BI "-[no]h"  "    no"
+ Print help info and quit
+
+.BI "-nice"  " int" " 19" 
+ Set the nicelevel
+
+.BI "-eignr"  " int" " 7" 
+ Eigenvector to use (first is 1)
+
+.BI "-temp"  " real" "    300" 
+ Temperature in Kelvin
+
+.BI "-amplitude"  " real" "   0.25" 
+ Amplitude for modes with eigenvalue=0
+
+.BI "-nframes"  " int" " 30" 
+ Number of frames to generate
+