1GMX-NMEIG(1)                        GROMACS                       GMX-NMEIG(1)
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NAME

6       gmx-nmeig - Diagonalize the Hessian for normal mode analysis
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SYNOPSIS

9          gmx nmeig [-f [<.mtx>]] [-s [<.tpr>]] [-of [<.xvg>]] [-ol [<.xvg>]]
10                    [-os [<.xvg>]] [-qc [<.xvg>]] [-v [<.trr/.cpt/...>]]
11                    [-xvg <enum>] [-[no]m] [-first <int>] [-last <int>]
12                    [-maxspec <int>] [-T <real>] [-P <real>] [-sigma <int>]
13                    [-scale <real>] [-linear_toler <real>] [-[no]constr]
14                    [-width <real>]
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DESCRIPTION

17       gmx  nmeig  calculates  the  eigenvectors/values of a (Hessian) matrix,
18       which can be calculated with gmx mdrun.  The eigenvectors  are  written
19       to  a  trajectory  file (-v).  The structure is written first with t=0.
20       The eigenvectors are written as frames with the eigenvector number  and
21       eigenvalue  written  as  step  number and timestamp, respectively.  The
22       eigenvectors can be analyzed with gmx anaeig.  An  ensemble  of  struc‐
23       tures  can be generated from the eigenvectors with gmx nmens. When mass
24       weighting is used, the generated eigenvectors will be  scaled  back  to
25       plain Cartesian coordinates before generating the output. In this case,
26       they will no longer be exactly orthogonal  in  the  standard  Cartesian
27       norm, but in the mass-weighted norm they would be.
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29       This  program  can be optionally used to compute quantum corrections to
30       heat capacity and enthalpy by providing an extra file argument  -qcorr.
31       See  the  GROMACS  manual,  Chapter 1, for details. The result includes
32       subtracting a harmonic degree of freedom at the given temperature.  The
33       total  correction  is  printed on the terminal screen.  The recommended
34       way of getting the corrections out is:
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36       gmx nmeig -s topol.tpr -f nm.mtx -first 7 -last 10000 -T 300 -qc [-con‐
37       str]
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39       The  -constr option should be used when bond constraints were used dur‐
40       ing the simulation for all the covalent bonds. If this is not the case,
41       you need to analyze the quant_corr.xvg file yourself.
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43       To  make  things more flexible, the program can also take virtual sites
44       into account when computing quantum corrections. When selecting -constr
45       and -qc, the -begin and -end options will be set automatically as well.
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47       Based  on  a  harmonic analysis of the normal mode frequencies, thermo‐
48       chemical properties S0 (Standard Entropy), Cv (Heat  capacity  at  con‐
49       stant  volume), Zero-point energy and the internal energy are computed,
50       much in the same manner as popular quantum chemistry programs.
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OPTIONS

53       Options to specify input files:
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55       -f [<.mtx>] (hessian.mtx)
56              Hessian matrix
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58       -s [<.tpr>] (topol.tpr)
59              Portable xdr run input file
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61       Options to specify output files:
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63       -of [<.xvg>] (eigenfreq.xvg)
64              xvgr/xmgr file
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66       -ol [<.xvg>] (eigenval.xvg)
67              xvgr/xmgr file
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69       -os [<.xvg>] (spectrum.xvg) (Optional)
70              xvgr/xmgr file
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72       -qc [<.xvg>] (quant_corr.xvg) (Optional)
73              xvgr/xmgr file
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75       -v [<.trr/.cpt/...>] (eigenvec.trr)
76              Full precision trajectory: trr cpt tng
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78       Other options:
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80       -xvg <enum> (xmgrace)
81              xvg plot formatting: xmgrace, xmgr, none
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83       -[no]m (yes)
84              Divide elements of Hessian by product of sqrt(mass) of  involved
85              atoms  prior to diagonalization. This should be used for 'Normal
86              Modes' analysis
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88       -first <int> (1)
89              First eigenvector to write away
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91       -last <int> (50)
92              Last eigenvector to write away. -1 is use all dimensions.
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94       -maxspec <int> (4000)
95              Highest frequency (1/cm) to consider in the spectrum
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97       -T <real> (298.15)
98              Temperature for computing entropy, quantum heat capacity and en‐
99              thalpy  when using normal mode calculations to correct classical
100              simulations
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102       -P <real> (1)
103              Pressure (bar) when computing entropy
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105       -sigma <int> (1)
106              Number of symmetric copies used when computing entropy. E.g. for
107              water the number is 2, for NH3 it is 3 and for methane it is 12.
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109       -scale <real> (1)
110              Factor  to  scale  frequencies  before computing thermochemistry
111              values
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113       -linear_toler <real> (1e-05)
114              Tolerance for determining whether a compound is linear as deter‐
115              mined from the ration of the moments inertion Ix/Iy and Ix/Iz.
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117       -[no]constr (no)
118              If constraints were used in the simulation but not in the normal
119              mode analysis you will need to set this for computing the  quan‐
120              tum corrections.
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122       -width <real> (1)
123              Width  (sigma)  of  the  gaussian peaks (1/cm) when generating a
124              spectrum
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SEE ALSO

127       gmx(1)
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129       More    information    about    GROMACS    is    available    at     <‐
130       http://www.gromacs.org/>.
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133       2022, GROMACS development team
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1382022.2                           Jun 16, 2022                     GMX-NMEIG(1)
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