gmx-nmeig(1) GROMACS Manual gmx-nmeig(1)NAMEgmx-nmeig - Diagonalize the Hessian for normal mode analysis
SYNOPSIS
gmx nmeig [-f [<.mtx>]] [-s [<.tpr/.tpb/...>]] [-of [<.xvg>]]
[-ol [<.xvg>]] [-os [<.xvg>]] [-qc [<.xvg>]]
[-v [<.trr/.cpt/...>]] [-nice <int>] [-xvg <enum>] [-[no]m]
[-first <int>] [-last <int>] [-maxspec <int>] [-T <real>]
[-[no]constr] [-width <real>]
DESCRIPTION
gmx nmeig calculates the eigenvectors/values of a (Hessian) matrix,
which can be calculated with gmx 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 time‐
stamp. The eigenvectors can be analyzed with gmx anaeig. An ensemble of
structures can be generated from the eigenvectors with gmx 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 Carte‐
sian norm, but in the mass-weighted norm they would be.
This program can be optionally used to compute quantum corrections to
heat capacity and enthalpy by providing an extra file argument -qcorr.
See the GROMACS manual, Chapter 1, for details. The result includes
subtracting a harmonic degree of freedom at the given temperature. The
total correction is printed on the terminal screen. The recommended way
of getting the corrections out is:
gmx nmeig -s topol.tpr -f nm.mtx -first 7 -last 10000 -T 300 -qc [-con‐
str]
The -constr option should be used when bond constraints were used dur‐
ing the simulation for all the covalent bonds. If this is not the case,
you need to analyze the quant_corr.xvg file yourself.
To make things more flexible, the program can also take virtual sites
into account when computing quantum corrections. When selecting -constr
and -qc, the -begin and -end options will be set automatically as well.
Again, if you think you know it better, please check the eigenfreq.xvg
output.
OPTIONS
Options to specify input and output files:
-f [<.mtx>] (hessian.mtx) (Input)
Hessian matrix
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa
-of [<.xvg>] (eigenfreq.xvg) (Output)
xvgr/xmgr file
-ol [<.xvg>] (eigenval.xvg) (Output)
xvgr/xmgr file
-os [<.xvg>] (spectrum.xvg) (Output, Optional)
xvgr/xmgr file
-qc [<.xvg>] (quant_corr.xvg) (Output, Optional)
xvgr/xmgr file
-v [<.trr/.cpt/...>] (eigenvec.trr) (Output)
Full precision trajectory: trr cpt trj tng
Other options:
-nice <int> (19)
Set the nicelevel
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-[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
-maxspec <int> (4000)
Highest frequency (1/cm) to consider in the spectrum
-T <real> (298.15)
Temperature for computing quantum heat capacity and enthalpy when
using normal mode calculations to correct classical simulations
-[no]constr (no)
If constraints were used in the simulation but not in the normal
mode analysis (this is the recommended way of doing it) you will need
to set this for computing the quantum corrections.
-width <real> (1)
Width (sigma) of the gaussian peaks (1/cm) when generating a spec‐
trum
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-nmeig(1)
