1GMX-ENEMAT(1)                       GROMACS                      GMX-ENEMAT(1)
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NAME

6       gmx-enemat - Extract an energy matrix from an energy file
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SYNOPSIS

9          gmx enemat [-f [<.edr>]] [-groups [<.dat>]] [-eref [<.dat>]]
10                     [-emat [<.xpm>]] [-etot [<.xvg>]] [-b <time>] [-e <time>]
11                     [-dt <time>] [-[no]w] [-xvg <enum>] [-[no]sum]
12                     [-skip <int>] [-[no]mean] [-nlevels <int>] [-max <real>]
13                     [-min <real>] [-[no]coulsr] [-[no]coul14] [-[no]ljsr]
14                     [-[no]lj14] [-[no]bhamsr] [-[no]free] [-temp <real>]
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DESCRIPTION

17       gmx  enemat  extracts an energy matrix from the energy file (-f).  With
18       -groups a file must be supplied with on each line a group of  atoms  to
19       be  used.  For  these  groups  matrix  of  interaction energies will be
20       extracted from the energy file by looking for energy groups with  names
21       corresponding  to  pairs  of groups of atoms, e.g. if your -groups file
22       contains:
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24          2
25          Protein
26          SOL
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28       then energy groups with names like ‘Coul-SR:Protein-SOL’  and  ‘LJ:Pro‐
29       tein-SOL’  are expected in the energy file (although gmx enemat is most
30       useful if many groups are analyzed simultaneously). Matrices  for  dif‐
31       ferent  energy  types  are written out separately, as controlled by the
32       -[no]coul, -[no]coulr, -[no]coul14, -[no]lj, -[no]lj14,  -[no]bham  and
33       -[no]free  options.   Finally,  the total interaction energy energy per
34       group can be calculated (-etot).
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36       An approximation of the free energy can be calculated using:  E_free  =
37       E_0  + kT log(<exp((E-E_0)/kT)>), where ‘<>’ stands for time-average. A
38       file with reference free energies can be supplied to calculate the free
39       energy  difference with some reference state. Group names (e.g. residue
40       names) in the reference file should correspond to the  group  names  as
41       used  in  the -groups file, but a appended number (e.g. residue number)
42       in the -groups will be ignored in the comparison.
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OPTIONS

45       Options to specify input files:
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47       -f [<.edr>] (ener.edr) (Optional)
48              Energy file
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50       -groups [<.dat>] (groups.dat)
51              Generic data file
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53       -eref [<.dat>] (eref.dat) (Optional)
54              Generic data file
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56       Options to specify output files:
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58       -emat [<.xpm>] (emat.xpm)
59              X PixMap compatible matrix file
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61       -etot [<.xvg>] (energy.xvg)
62              xvgr/xmgr file
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64       Other options:
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66       -b <time> (0)
67              Time of first frame to read from trajectory (default unit ps)
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69       -e <time> (0)
70              Time of last frame to read from trajectory (default unit ps)
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72       -dt <time> (0)
73              Only use frame when t MOD dt = first time (default unit ps)
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75       -[no]w (no)
76              View output .xvg, .xpm, .eps and .pdb files
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78       -xvg <enum> (xmgrace)
79              xvg plot formatting: xmgrace, xmgr, none
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81       -[no]sum (no)
82              Sum the energy terms selected rather than display them all
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84       -skip <int> (0)
85              Skip number of frames between data points
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87       -[no]mean (yes)
88              with -groups extracts matrix of mean energies instead of  matrix
89              for each timestep
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91       -nlevels <int> (20)
92              number of levels for matrix colors
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94       -max <real> (1e+20)
95              max value for energies
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97       -min <real> (-1e+20)
98              min value for energies
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100       -[no]coulsr (yes)
101              extract Coulomb SR energies
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103       -[no]coul14 (no)
104              extract Coulomb 1-4 energies
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106       -[no]ljsr (yes)
107              extract Lennard-Jones SR energies
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109       -[no]lj14 (no)
110              extract Lennard-Jones 1-4 energies
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112       -[no]bhamsr (no)
113              extract Buckingham SR energies
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115       -[no]free (yes)
116              calculate free energy
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118       -temp <real> (300)
119              reference temperature for free energy calculation
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SEE ALSO

122       gmx(1)
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124       More     information    about    GROMACS    is    available    at    <‐
125       http://www.gromacs.org/>.
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128       2019, GROMACS development team
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1332018.7                           May 29, 2019                    GMX-ENEMAT(1)
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