1g_energy(1) GROMACS suite, VERSION 4.5 g_energy(1)
2
6 g_energy - writes energies to xvg files and displays averages
7 VERSION 4.5
9
11 g_energy -f ener.edr -f2 ener.edr -s topol.tpr -o energy.xvg -viol
12 violaver.xvg -pairs pairs.xvg -ora orienta.xvg -ort orientt.xvg -oda
13 orideva.xvg -odr oridevr.xvg -odt oridevt.xvg -oten oriten.xvg -corr
14 enecorr.xvg -vis visco.xvg -ravg runavgdf.xvg -[no]h -[no]version -nice
15 int -b time -e time -[no]w -xvg enum -[no]fee -fetemp real -zero real
16 -[no]sum -[no]dp -nbmin int -nbmax int -[no]mutot -skip int -[no]aver
17 -nmol int -nconstr int -[no]fluc -[no]orinst -[no]ovec -acflen int
18 -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit
19 real
20
22 g_energy extracts energy components or distance restraint data from an
23 energy file. The user is prompted to interactively select the energy
24 terms she wants.
25 Average, RMSD and drift are calculated with full precision from the
28 simulation (see printed manual). Drift is calculated by performing a
29 LSQ fit of the data to a straight line. The reported total drift is the
30 difference of the fit at the first and last point. An error estimate
31 of the average is given based on a block averages over 5 blocks using
32 the full precision averages. The error estimate can be performed over
33 multiple block lengths with the options -nbmin and -nbmax. Note that
34 in most cases the energy files contains averages over all MD steps, or
35 over many more points than the number of frames in energy file. This
36 makes the g_energy statistics output more accurate than the xvg output.
37 When exact averages are not present in the energy file the statistics
38 mentioned above is simply over the single, per-frame energy values.
39 The term fluctuation gives the RMSD around the LSQ fit.
42 Some fluctuation-dependent properties can be calculated provided the
45 correct energy terms are selected. The following properties will be
46 computed:
47 Property Energy terms needed
49 ---------------------------------------------------
51 Heat capacity Cp (NPT sims): Enthalpy, Temp
53 Heat capacity Cv (NVT sims): Etot, Temp
55 Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp
57 Isothermal compressibility: Vol, Temp
59 Adiabatic bulk modulus: Vol, Temp
61 ---------------------------------------------------
63 You always need to set the number of molecules -nmol, and, if you used
65 constraints in your simulations you will need to give the number of
66 constraints per molecule -nconstr in order to correct for this: (ncon‐
67 str/2) kB is subtracted from the heat capacity in this case. For
68 instance in the case of rigid water you need to give the value 3 to
69 this option.
70 When the -viol option is set, the time averaged violations are plotted
73 and the running time-averaged and instantaneous sum of violations are
74 recalculated. Additionally running time-averaged and instantaneous dis‐
75 tances between selected pairs can be plotted with the -pairs option.
76 Options -ora, -ort, -oda, -odr and -odt are used for analyzing
79 orientation restraint data. The first two options plot the orienta‐
80 tion, the last three the deviations of the orientations from the exper‐
81 imental values. The options that end on an 'a' plot the average over
82 time as a function of restraint. The options that end on a 't' prompt
83 the user for restraint label numbers and plot the data as a function of
84 time. Option -odr plots the RMS deviation as a function of restraint.
85 When the run used time or ensemble averaged orientation restraints,
86 option -orinst can be used to analyse the instantaneous, not ensem‐
87 ble-averaged orientations and deviations instead of the time and ensem‐
88 ble averages.
89 Option -oten plots the eigenvalues of the molecular order tensor for
92 each orientation restraint experiment. With option -ovec also the
93 eigenvectors are plotted.
94 With -fee an estimate is calculated for the free-energy difference
97 with an ideal gas state:
98 Delta A = A(N,V,T) - A_idgas(N,V,T) = kT ln e(Upot/kT)
100 Delta G = G(N,p,T) - G_idgas(N,p,T) = kT ln e(Upot/kT)
102 where k is Boltzmann's constant, T is set by -fetemp and the average
104 is over the ensemble (or time in a trajectory). Note that this is in
105 principle only correct when averaging over the whole (Boltzmann) ensem‐
106 ble and using the potential energy. This also allows for an entropy
107 estimate using:
108 Delta S(N,V,T) = S(N,V,T) - S_idgas(N,V,T) = (Upot - Delta A)/T
110 Delta S(N,p,T) = S(N,p,T) - S_idgas(N,p,T) = (Upot + pV - Delta G)/T
112 When a second energy file is specified ( -f2), a free energy difference
115 is calculated dF = -kT ln e -(EB-EA)/kT A , where EA and EB are the
116 energies from the first and second energy files, and the average is
117 over the ensemble A. NOTE that the energies must both be calculated
118 from the same trajectory.
119
121 -f ener.edr Input
122 Energy file
123 -f2 ener.edr Input, Opt.
125 Energy file
126 -s topol.tpr Input, Opt.
128 Run input file: tpr tpb tpa
129 -o energy.xvg Output
131 xvgr/xmgr file
132 -viol violaver.xvg Output, Opt.
134 xvgr/xmgr file
135 -pairs pairs.xvg Output, Opt.
137 xvgr/xmgr file
138 -ora orienta.xvg Output, Opt.
140 xvgr/xmgr file
141 -ort orientt.xvg Output, Opt.
143 xvgr/xmgr file
144 -oda orideva.xvg Output, Opt.
146 xvgr/xmgr file
147 -odr oridevr.xvg Output, Opt.
149 xvgr/xmgr file
150 -odt oridevt.xvg Output, Opt.
152 xvgr/xmgr file
153 -oten oriten.xvg Output, Opt.
155 xvgr/xmgr file
156 -corr enecorr.xvg Output, Opt.
158 xvgr/xmgr file
159 -vis visco.xvg Output, Opt.
161 xvgr/xmgr file
162 -ravg runavgdf.xvg Output, Opt.
164 xvgr/xmgr file
165
168 -[no]hno
169 Print help info and quit
170 -[no]versionno
172 Print version info and quit
173 -nice int 19
175 Set the nicelevel
176 -b time 0
178 First frame (ps) to read from trajectory
179 -e time 0
181 Last frame (ps) to read from trajectory
182 -[no]wno
184 View output xvg, xpm, eps and pdb files
185 -xvg enum xmgrace
187 xvg plot formatting: xmgrace, xmgr or none
188 -[no]feeno
190 Do a free energy estimate
191 -fetemp real 300
193 Reference temperature for free energy calculation
194 -zero real 0
196 Subtract a zero-point energy
197 -[no]sumno
199 Sum the energy terms selected rather than display them all
200 -[no]dpno
202 Print energies in high precision
203 -nbmin int 5
205 Minimum number of blocks for error estimate
206 -nbmax int 5
208 Maximum number of blocks for error estimate
209 -[no]mutotno
211 Compute the total dipole moment from the components
212 -skip int 0
214 Skip number of frames between data points
215 -[no]averno
217 Also print the exact average and rmsd stored in the energy frames
218 (only when 1 term is requested)
219 -nmol int 1
221 Number of molecules in your sample: the energies are divided by this
222 number
223 -nconstr int 0
225 Number of constraints per molecule. Necessary for calculating the heat
226 capacity
227 -[no]flucno
229 Calculate autocorrelation of energy fluctuations rather than energy
230 itself
231 -[no]orinstno
233 Analyse instantaneous orientation data
234 -[no]ovecno
236 Also plot the eigenvectors with -oten
237 -acflen int -1
239 Length of the ACF, default is half the number of frames
240 -[no]normalizeyes
242 Normalize ACF
243 -P enum 0
245 Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or
246 3
247 -fitfn enum none
249 Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7 or
250 exp9
251 -ncskip int 0
253 Skip N points in the output file of correlation functions
254 -beginfit real 0
256 Time where to begin the exponential fit of the correlation function
257 -endfit real -1
259 Time where to end the exponential fit of the correlation function, -1
260 is until the end
261
264 gromacs(7)
265 More information about GROMACS is available at <http://www.gro‐
267 macs.org/>.
268 Thu 26 Aug 2010 g_energy(1)