1GMX-ENERGY(1) GROMACS GMX-ENERGY(1)
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6 gmx-energy - Writes energies to xvg files and display averages
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9 gmx energy [-f [<.edr>]] [-f2 [<.edr>]] [-s [<.tpr>]] [-o [<.xvg>]]
10 [-viol [<.xvg>]] [-pairs [<.xvg>]] [-corr [<.xvg>]]
11 [-vis [<.xvg>]] [-evisco [<.xvg>]] [-eviscoi [<.xvg>]]
12 [-ravg [<.xvg>]] [-odh [<.xvg>]] [-b <time>] [-e <time>]
13 [-[no]w] [-xvg <enum>] [-[no]fee] [-fetemp <real>]
14 [-zero <real>] [-[no]sum] [-[no]dp] [-nbmin <int>]
15 [-nbmax <int>] [-[no]mutot] [-[no]aver] [-nmol <int>]
16 [-[no]fluct_props] [-[no]driftcorr] [-[no]fluc]
17 [-[no]orinst] [-[no]ovec] [-acflen <int>] [-[no]normalize]
18 [-P <enum>] [-fitfn <enum>] [-beginfit <real>]
19 [-endfit <real>]
20
22 gmx energy extracts energy components from an energy file. The user is
23 prompted to interactively select the desired energy terms.
24 Average, RMSD, and drift are calculated with full precision from the
26 simulation (see printed manual). Drift is calculated by performing a
27 least-squares fit of the data to a straight line. The reported total
28 drift is the difference of the fit at the first and last point. An er‐
29 ror estimate of the average is given based on a block averages over 5
30 blocks using the full-precision averages. The error estimate can be
31 performed over multiple block lengths with the options -nbmin and
32 -nbmax. Note that in most cases the energy files contains averages
33 over all MD steps, or over many more points than the number of frames
34 in energy file. This makes the gmx energy statistics output more accu‐
35 rate than the .xvg output. When exact averages are not present in the
36 energy file, the statistics mentioned above are simply over the single,
37 per-frame energy values.
38 The term fluctuation gives the RMSD around the least-squares fit.
40 Some fluctuation-dependent properties can be calculated provided the
42 correct energy terms are selected, and that the command line option
43 -fluct_props is given. The following properties will be computed:
44 ┌───────────────────────────┬─────────────────────┐
46 │Property │ Energy terms needed │
47 ├───────────────────────────┼─────────────────────┤
48 │Heat capacity C_p (NPT │ Enthalpy, Temp │
49 │sims): │ │
50 ├───────────────────────────┼─────────────────────┤
51 │Heat capacity C_v (NVT │ Etot, Temp │
52 │sims): │ │
53 ├───────────────────────────┼─────────────────────┤
54 │Thermal expansion coeff. │ Enthalpy, Vol, Temp │
55 │(NPT): │ │
56 ├───────────────────────────┼─────────────────────┤
57 │Isothermal compressibil‐ │ Vol, Temp │
58 │ity: │ │
59 ├───────────────────────────┼─────────────────────┤
60 │Adiabatic bulk modulus: │ Vol, Temp │
61 └───────────────────────────┴─────────────────────┘
62 You always need to set the number of molecules -nmol. The C_p/C_v com‐
64 putations do not include any corrections for quantum effects. Use the
65 gmx dos program if you need that (and you do).
66 Option -odh extracts and plots the free energy data (Hamiltoian differ‐
68 ences and/or the Hamiltonian derivative dhdl) from the ener.edr file.
69 With -fee an estimate is calculated for the free-energy difference with
71 an ideal gas state:
72 Delta A = A(N,V,T) - A_idealgas(N,V,T) = kT
74 ln(<exp(U_pot/kT)>)
75 Delta G = G(N,p,T) - G_idealgas(N,p,T) = kT
76 ln(<exp(U_pot/kT)>)
77 where k is Boltzmann's constant, T is set by -fetemp and the average is
79 over the ensemble (or time in a trajectory). Note that this is in
80 principle only correct when averaging over the whole (Boltzmann) ensem‐
81 ble and using the potential energy. This also allows for an entropy es‐
82 timate using:
83 Delta S(N,V,T) = S(N,V,T) - S_idealgas(N,V,T) =
85 (<U_pot> - Delta A)/T
86 Delta S(N,p,T) = S(N,p,T) - S_idealgas(N,p,T) =
87 (<U_pot> + pV - Delta G)/T
88 When a second energy file is specified (-f2), a free energy difference
90 is calculated:
91 dF = -kT
93 ln(<exp(-(E_B-E_A) /
94 kT)>_A),
95 where E_A and E_B are the energies from the first and second energy
97 files, and the average is over the ensemble A. The running average of
98 the free energy difference is printed to a file specified by -ravg.
99 Note that the energies must both be calculated from the same trajec‐
100 tory.
101
103 Options to specify input files:
104 -f [<.edr>] (ener.edr)
106 Energy file
107 -f2 [<.edr>] (ener.edr) (Optional)
109 Energy file
110 -s [<.tpr>] (topol.tpr) (Optional)
112 Portable xdr run input file
113 Options to specify output files:
115 -o [<.xvg>] (energy.xvg)
117 xvgr/xmgr file
118 -viol [<.xvg>] (violaver.xvg) (Optional)
120 xvgr/xmgr file
121 -pairs [<.xvg>] (pairs.xvg) (Optional)
123 xvgr/xmgr file
124 -corr [<.xvg>] (enecorr.xvg) (Optional)
126 xvgr/xmgr file
127 -vis [<.xvg>] (visco.xvg) (Optional)
129 xvgr/xmgr file
130 -evisco [<.xvg>] (evisco.xvg) (Optional)
132 xvgr/xmgr file
133 -eviscoi [<.xvg>] (eviscoi.xvg) (Optional)
135 xvgr/xmgr file
136 -ravg [<.xvg>] (runavgdf.xvg) (Optional)
138 xvgr/xmgr file
139 -odh [<.xvg>] (dhdl.xvg) (Optional)
141 xvgr/xmgr file
142 Other options:
144 -b <time> (0)
146 Time of first frame to read from trajectory (default unit ps)
147 -e <time> (0)
149 Time of last frame to read from trajectory (default unit ps)
150 -[no]w (no)
152 View output .xvg, .xpm, .eps and .pdb files
153 -xvg <enum> (xmgrace)
155 xvg plot formatting: xmgrace, xmgr, none
156 -[no]fee (no)
158 Do a free energy estimate
159 -fetemp <real> (300)
161 Reference temperature for free energy calculation
162 -zero <real> (0)
164 Subtract a zero-point energy
165 -[no]sum (no)
167 Sum the energy terms selected rather than display them all
168 -[no]dp (no)
170 Print energies in high precision
171 -nbmin <int> (5)
173 Minimum number of blocks for error estimate
174 -nbmax <int> (5)
176 Maximum number of blocks for error estimate
177 -[no]mutot (no)
179 Compute the total dipole moment from the components
180 -[no]aver (no)
182 Also print the exact average and rmsd stored in the energy
183 frames (only when 1 term is requested)
184 -nmol <int> (1)
186 Number of molecules in your sample: the energies are divided by
187 this number
188 -[no]fluct_props (no)
190 Compute properties based on energy fluctuations, like heat ca‐
191 pacity
192 -[no]driftcorr (no)
194 Useful only for calculations of fluctuation properties. The
195 drift in the observables will be subtracted before computing the
196 fluctuation properties.
197 -[no]fluc (no)
199 Calculate autocorrelation of energy fluctuations rather than en‐
200 ergy itself
201 -[no]orinst (no)
203 Analyse instantaneous orientation data
204 -[no]ovec (no)
206 Also plot the eigenvectors with -oten
207 -acflen <int> (-1)
209 Length of the ACF, default is half the number of frames
210 -[no]normalize (yes)
212 Normalize ACF
213 -P <enum> (0)
215 Order of Legendre polynomial for ACF (0 indicates none): 0, 1,
216 2, 3
217 -fitfn <enum> (none)
219 Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
220 -beginfit <real> (0)
222 Time where to begin the exponential fit of the correlation func‐
223 tion
224 -endfit <real> (-1)
226 Time where to end the exponential fit of the correlation func‐
227 tion, -1 is until the end
228
230 gmx(1)
231 More information about GROMACS is available at <‐
233 http://www.gromacs.org/>.
234
236 2022, GROMACS development team
2372022.3 Sep 02, 2022 GMX-ENERGY(1)