1g_enemat(1) GROMACS suite, VERSION 4.5 g_enemat(1)
2
6 g_enemat - extracts an energy matrix from an energy file
7 VERSION 4.5
9
11 g_enemat -f ener.edr -groups groups.dat -eref eref.dat -emat emat.xpm
12 -etot energy.xvg -[no]h -[no]version -nice int -b time -e time -dt time
13 -[no]w -xvg enum -[no]sum -skip int -[no]mean -nlevels int -max real
14 -min real -[no]coul -[no]coulr -[no]coul14 -[no]lj -[no]lj -[no]lj14
15 -[no]bhamsr -[no]bhamlr -[no]free -temp real
16
18 g_enemat extracts an energy matrix from the energy file ( -f). With
19 -groups a file must be supplied with on each line a group of atoms to
20 be used. For these groups matrix of interaction energies will be
21 extracted from the energy file by looking for energy groups with names
22 corresponding to pairs of groups of atoms. E.g. if your -groups file
23 contains:
24 2
26 Protein
28 SOL
30 then energy groups with names like 'Coul-SR:Protein-SOL' and 'LJ:Pro‐
32 tein-SOL' are expected in the energy file (although g_enemat is most
33 useful if many groups are analyzed simultaneously). Matrices for dif‐
34 ferent energy types are written out separately, as controlled by the
35 -[no]coul, -[no]coulr, -[no]coul14, -[no]lj, -[no]lj14, -[no]bham
36 and -[no]free options. Finally, the total interaction energy energy
37 per group can be calculated ( -etot).
38 An approximation of the free energy can be calculated using: E(free) =
41 E0 + kT log( exp((E-E0)/kT) ), where '' stands for time-average. A file
42 with reference free energies can be supplied to calculate the free
43 energy difference with some reference state. Group names (e.g. residue
44 names) in the reference file should correspond to the group names as
45 used in the -groups file, but a appended number (e.g. residue number)
46 in the -groups will be ignored in the comparison.
47
49 -f ener.edr Input, Opt.
50 Energy file
51 -groups groups.dat Input
53 Generic data file
54 -eref eref.dat Input, Opt.
56 Generic data file
57 -emat emat.xpm Output
59 X PixMap compatible matrix file
60 -etot energy.xvg Output
62 xvgr/xmgr file
63
66 -[no]hno
67 Print help info and quit
68 -[no]versionno
70 Print version info and quit
71 -nice int 19
73 Set the nicelevel
74 -b time 0
76 First frame (ps) to read from trajectory
77 -e time 0
79 Last frame (ps) to read from trajectory
80 -dt time 0
82 Only use frame when t MOD dt = first time (ps)
83 -[no]wno
85 View output xvg, xpm, eps and pdb files
86 -xvg enum xmgrace
88 xvg plot formatting: xmgrace, xmgr or none
89 -[no]sumno
91 Sum the energy terms selected rather than display them all
92 -skip int 0
94 Skip number of frames between data points
95 -[no]meanyes
97 with -groups extracts matrix of mean energies instead of matrix for
98 each timestep
99 -nlevels int 20
101 number of levels for matrix colors
102 -max real 1e+20
104 max value for energies
105 -min real -1e+20
107 min value for energies
108 -[no]coulyes
110 extract Coulomb SR energies
111 -[no]coulrno
113 extract Coulomb LR energies
114 -[no]coul14no
116 extract Coulomb 1-4 energies
117 -[no]ljyes
119 extract Lennard-Jones SR energies
120 -[no]ljno
122 extract Lennard-Jones LR energies
123 -[no]lj14no
125 extract Lennard-Jones 1-4 energies
126 -[no]bhamsrno
128 extract Buckingham SR energies
129 -[no]bhamlrno
131 extract Buckingham LR energies
132 -[no]freeyes
134 calculate free energy
135 -temp real 300
137 reference temperature for free energy calculation
138
141 gromacs(7)
142 More information about GROMACS is available at <http://www.gro‐
144 macs.org/>.
145 Thu 26 Aug 2010 g_enemat(1)