1GMX-NMEIG(1) GROMACS GMX-NMEIG(1)
2
6 gmx-nmeig - Diagonalize the Hessian for normal mode analysis
7
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>]
15
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.
28 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:
35 gmx nmeig -s topol.tpr -f nm.mtx -first 7 -last 10000 -T 300 -qc [-con‐
37 str]
38 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.
42 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.
46 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.
51
53 Options to specify input files:
54 -f [<.mtx>] (hessian.mtx)
56 Hessian matrix
57 -s [<.tpr>] (topol.tpr)
59 Portable xdr run input file
60 Options to specify output files:
62 -of [<.xvg>] (eigenfreq.xvg)
64 xvgr/xmgr file
65 -ol [<.xvg>] (eigenval.xvg)
67 xvgr/xmgr file
68 -os [<.xvg>] (spectrum.xvg) (Optional)
70 xvgr/xmgr file
71 -qc [<.xvg>] (quant_corr.xvg) (Optional)
73 xvgr/xmgr file
74 -v [<.trr/.cpt/...>] (eigenvec.trr)
76 Full precision trajectory: trr cpt tng
77 Other options:
79 -xvg <enum> (xmgrace)
81 xvg plot formatting: xmgrace, xmgr, none
82 -[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
87 -first <int> (1)
89 First eigenvector to write away
90 -last <int> (50)
92 Last eigenvector to write away. -1 is use all dimensions.
93 -maxspec <int> (4000)
95 Highest frequency (1/cm) to consider in the spectrum
96 -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
101 -P <real> (1)
103 Pressure (bar) when computing entropy
104 -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.
108 -scale <real> (1)
110 Factor to scale frequencies before computing thermochemistry
111 values
112 -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.
116 -[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.
121 -width <real> (1)
123 Width (sigma) of the gaussian peaks (1/cm) when generating a
124 spectrum
125
127 gmx(1)
128 More information about GROMACS is available at <‐
130 http://www.gromacs.org/>.
131
133 2022, GROMACS development team
1342022.3 Sep 02, 2022 GMX-NMEIG(1)