This is the command gmx-nmeig that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
gmx-nmeig - Diagonalize the Hessian for normal mode analysis
SYNOPSIS
gmx nmeig [-f [<.mtx>]] [-s [<.tpr>]] [-of [<.xvg>]] [-ol [<.xvg>]]
[-os [<.xvg>]] [-qc [<.xvg>]] [-v [<.trr/.cpt/...>]]
[-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 timestamp. 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 Cartesian 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 [-constr]
The -constr option should be used when bond constraints were used during 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 files:
-f [<.mtx>] (hessian.mtx)
Hessian matrix
-s [<.tpr>] (topol.tpr)
Portable xdr run input file
Options to specify output files:
-of [<.xvg>] (eigenfreq.xvg)
xvgr/xmgr file
-ol [<.xvg>] (eigenval.xvg)
xvgr/xmgr file
-os [<.xvg>] (spectrum.xvg) (Optional)
xvgr/xmgr file
-qc [<.xvg>] (quant_corr.xvg) (Optional)
xvgr/xmgr file
-v [<.trr/.cpt/...>] (eigenvec.trr)
Full precision trajectory: trr cpt tng
Other options:
-xvg <enum>
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 spectrum
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