1GMX-NMEIG(1) GROMACS GMX-NMEIG(1)
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6 gmx-nmeig - Diagonalize the Hessian for normal mode analysis
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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>] [-[no]constr] [-width <real>]
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15 gmx nmeig calculates the eigenvectors/values of a (Hessian) matrix,
16 which can be calculated with gmx mdrun. The eigenvectors are written
17 to a trajectory file (-v). The structure is written first with t=0.
18 The eigenvectors are written as frames with the eigenvector number and
19 eigenvalue written as step number and timestamp, respectively. The
20 eigenvectors can be analyzed with gmx anaeig. An ensemble of struc‐
21 tures can be generated from the eigenvectors with gmx nmens. When mass
22 weighting is used, the generated eigenvectors will be scaled back to
23 plain Cartesian coordinates before generating the output. In this case,
24 they will no longer be exactly orthogonal in the standard Cartesian
25 norm, but in the mass-weighted norm they would be.
26 This program can be optionally used to compute quantum corrections to
28 heat capacity and enthalpy by providing an extra file argument -qcorr.
29 See the GROMACS manual, Chapter 1, for details. The result includes
30 subtracting a harmonic degree of freedom at the given temperature. The
31 total correction is printed on the terminal screen. The recommended
32 way of getting the corrections out is:
33 gmx nmeig -s topol.tpr -f nm.mtx -first 7 -last 10000 -T 300 -qc [-con‐
35 str]
36 The -constr option should be used when bond constraints were used dur‐
38 ing the simulation for all the covalent bonds. If this is not the case,
39 you need to analyze the quant_corr.xvg file yourself.
40 To make things more flexible, the program can also take virtual sites
42 into account when computing quantum corrections. When selecting -constr
43 and -qc, the -begin and -end options will be set automatically as well.
44 Again, if you think you know it better, please check the eigenfreq.xvg
45 output.
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48 Options to specify input files:
49 -f [<.mtx>] (hessian.mtx)
51 Hessian matrix
52 -s [<.tpr>] (topol.tpr)
54 Portable xdr run input file
55 Options to specify output files:
57 -of [<.xvg>] (eigenfreq.xvg)
59 xvgr/xmgr file
60 -ol [<.xvg>] (eigenval.xvg)
62 xvgr/xmgr file
63 -os [<.xvg>] (spectrum.xvg) (Optional)
65 xvgr/xmgr file
66 -qc [<.xvg>] (quant_corr.xvg) (Optional)
68 xvgr/xmgr file
69 -v [<.trr/.cpt/…>] (eigenvec.trr)
71 Full precision trajectory: trr cpt tng
72 Other options:
74 -xvg <enum> (xmgrace)
76 xvg plot formatting: xmgrace, xmgr, none
77 -[no]m (yes)
79 Divide elements of Hessian by product of sqrt(mass) of involved
80 atoms prior to diagonalization. This should be used for ‘Normal
81 Modes’ analysis
82 -first <int> (1)
84 First eigenvector to write away
85 -last <int> (50)
87 Last eigenvector to write away
88 -maxspec <int> (4000)
90 Highest frequency (1/cm) to consider in the spectrum
91 -T <real> (298.15)
93 Temperature for computing quantum heat capacity and enthalpy
94 when using normal mode calculations to correct classical simula‐
95 tions
96 -[no]constr (no)
98 If constraints were used in the simulation but not in the normal
99 mode analysis (this is the recommended way of doing it) you will
100 need to set this for computing the quantum corrections.
101 -width <real> (1)
103 Width (sigma) of the gaussian peaks (1/cm) when generating a
104 spectrum
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107 gmx(1)
108 More information about GROMACS is available at <‐
110 http://www.gromacs.org/>.
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113 2019, GROMACS development team
1142018.7 May 29, 2019 GMX-NMEIG(1)