1 .TH g_enemat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
3 g_enemat - extracts an energy matrix from an energy file
5 .B VERSION 4.5.4-dev-20110404-bc5695c
9 .BI "\-groups" " groups.dat "
10 .BI "\-eref" " eref.dat "
11 .BI "\-emat" " emat.xpm "
12 .BI "\-etot" " energy.xvg "
14 .BI "\-[no]version" ""
24 .BI "\-nlevels" " int "
38 \&\fB g_enemat\fR extracts an energy matrix from the energy file (\fB \-f\fR).
39 \&With \fB \-groups\fR a file must be supplied with on each
40 \&line a group of atoms to be used. For these groups matrix of
41 \&interaction energies will be extracted from the energy file
42 \&by looking for energy groups with names corresponding to pairs
43 \&of groups of atoms, e.g. if your \fB \-groups\fR file contains:
51 \&then energy groups with names like 'Coul\-SR:Protein\-SOL' and
52 \&'LJ:Protein\-SOL' are expected in the energy file (although
53 \&\fB g_enemat\fR is most useful if many groups are analyzed
54 \&simultaneously). Matrices for different energy types are written
55 \&out separately, as controlled by the
56 \&\fB \-[no]coul\fR, \fB \-[no]coulr\fR, \fB \-[no]coul14\fR,
57 \&\fB \-[no]lj\fR, \fB \-[no]lj14\fR,
58 \&\fB \-[no]bham\fR and \fB \-[no]free\fR options.
59 \&Finally, the total interaction energy energy per group can be
60 \&calculated (\fB \-etot\fR).
63 \&An approximation of the free energy can be calculated using:
64 \&E(free) = E0 + kT log( exp((E\-E0)/kT) ), where ''
65 \&stands for time\-average. A file with reference free energies
66 \&can be supplied to calculate the free energy difference
67 \&with some reference state. Group names (e.g. residue names)
68 \&in the reference file should correspond to the group names
69 \&as used in the \fB \-groups\fR file, but a appended number
70 \&(e.g. residue number) in the \fB \-groups\fR will be ignored
77 .BI "\-groups" " groups.dat"
81 .BI "\-eref" " eref.dat"
85 .BI "\-emat" " emat.xpm"
87 X PixMap compatible matrix file
89 .BI "\-etot" " energy.xvg"
95 Print help info and quit
97 .BI "\-[no]version" "no "
98 Print version info and quit
100 .BI "\-nice" " int" " 19"
103 .BI "\-b" " time" " 0 "
104 First frame (ps) to read from trajectory
106 .BI "\-e" " time" " 0 "
107 Last frame (ps) to read from trajectory
109 .BI "\-dt" " time" " 0 "
110 Only use frame when t MOD dt = first time (ps)
113 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
115 .BI "\-xvg" " enum" " xmgrace"
116 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
118 .BI "\-[no]sum" "no "
119 Sum the energy terms selected rather than display them all
121 .BI "\-skip" " int" " 0"
122 Skip number of frames between data points
124 .BI "\-[no]mean" "yes "
125 with \fB \-groups\fR extracts matrix of mean energies instead of matrix for each timestep
127 .BI "\-nlevels" " int" " 20"
128 number of levels for matrix colors
130 .BI "\-max" " real" " 1e+20 "
131 max value for energies
133 .BI "\-min" " real" " \-1e+20"
134 min value for energies
136 .BI "\-[no]coul" "yes "
137 extract Coulomb SR energies
139 .BI "\-[no]coulr" "no "
140 extract Coulomb LR energies
142 .BI "\-[no]coul14" "no "
143 extract Coulomb 1\-4 energies
145 .BI "\-[no]lj" "yes "
146 extract Lennard\-Jones SR energies
149 extract Lennard\-Jones LR energies
151 .BI "\-[no]lj14" "no "
152 extract Lennard\-Jones 1\-4 energies
154 .BI "\-[no]bhamsr" "no "
155 extract Buckingham SR energies
157 .BI "\-[no]bhamlr" "no "
158 extract Buckingham LR energies
160 .BI "\-[no]free" "yes "
161 calculate free energy
163 .BI "\-temp" " real" " 300 "
164 reference temperature for free energy calculation
169 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.