1GMX-ENERGY(1) GROMACS GMX-ENERGY(1)
2
6 gmx-energy - Writes energies to xvg files and display averages
7
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] [-skip <int>] [-[no]aver]
16 [-nmol <int>] [-[no]fluct_props] [-[no]driftcorr]
17 [-[no]fluc] [-[no]orinst] [-[no]ovec] [-acflen <int>]
18 [-[no]normalize] [-P <enum>] [-fitfn <enum>]
19 [-beginfit <real>] [-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
29 error 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 ln(<exp(U_pot/kT)>)
74 Delta G = G(N,p,T) - G_idealgas(N,p,T) = kT ln(<exp(U_pot/kT)>)
75 where k is Boltzmann’s constant, T is set by -fetemp and the average is
77 over the ensemble (or time in a trajectory). Note that this is in
78 principle only correct when averaging over the whole (Boltzmann) ensem‐
79 ble and using the potential energy. This also allows for an entropy
80 estimate using:
81 Delta S(N,V,T) = S(N,V,T) - S_idealgas(N,V,T) = (<U_pot> - Delta A)/T
83 Delta S(N,p,T) = S(N,p,T) - S_idealgas(N,p,T) = (<U_pot> + pV - Delta G)/T
84 When a second energy file is specified (-f2), a free energy difference
86 is calculated:
87 dF = -kT ln(<exp(-(E_B-E_A)/kT)>_A) ,
89 where E_A and E_B are the energies from the first and second energy
91 files, and the average is over the ensemble A. The running average of
92 the free energy difference is printed to a file specified by -ravg.
93 Note that the energies must both be calculated from the same trajec‐
94 tory.
95
97 Options to specify input files:
98 -f [<.edr>] (ener.edr)
100 Energy file
101 -f2 [<.edr>] (ener.edr) (Optional)
103 Energy file
104 -s [<.tpr>] (topol.tpr) (Optional)
106 Portable xdr run input file
107 Options to specify output files:
109 -o [<.xvg>] (energy.xvg)
111 xvgr/xmgr file
112 -viol [<.xvg>] (violaver.xvg) (Optional)
114 xvgr/xmgr file
115 -pairs [<.xvg>] (pairs.xvg) (Optional)
117 xvgr/xmgr file
118 -corr [<.xvg>] (enecorr.xvg) (Optional)
120 xvgr/xmgr file
121 -vis [<.xvg>] (visco.xvg) (Optional)
123 xvgr/xmgr file
124 -evisco [<.xvg>] (evisco.xvg) (Optional)
126 xvgr/xmgr file
127 -eviscoi [<.xvg>] (eviscoi.xvg) (Optional)
129 xvgr/xmgr file
130 -ravg [<.xvg>] (runavgdf.xvg) (Optional)
132 xvgr/xmgr file
133 -odh [<.xvg>] (dhdl.xvg) (Optional)
135 xvgr/xmgr file
136 Other options:
138 -b <time> (0)
140 Time of first frame to read from trajectory (default unit ps)
141 -e <time> (0)
143 Time of last frame to read from trajectory (default unit ps)
144 -[no]w (no)
146 View output .xvg, .xpm, .eps and .pdb files
147 -xvg <enum> (xmgrace)
149 xvg plot formatting: xmgrace, xmgr, none
150 -[no]fee (no)
152 Do a free energy estimate
153 -fetemp <real> (300)
155 Reference temperature for free energy calculation
156 -zero <real> (0)
158 Subtract a zero-point energy
159 -[no]sum (no)
161 Sum the energy terms selected rather than display them all
162 -[no]dp (no)
164 Print energies in high precision
165 -nbmin <int> (5)
167 Minimum number of blocks for error estimate
168 -nbmax <int> (5)
170 Maximum number of blocks for error estimate
171 -[no]mutot (no)
173 Compute the total dipole moment from the components
174 -skip <int> (0)
176 Skip number of frames between data points
177 -[no]aver (no)
179 Also print the exact average and rmsd stored in the energy
180 frames (only when 1 term is requested)
181 -nmol <int> (1)
183 Number of molecules in your sample: the energies are divided by
184 this number
185 -[no]fluct_props (no)
187 Compute properties based on energy fluctuations, like heat
188 capacity
189 -[no]driftcorr (no)
191 Useful only for calculations of fluctuation properties. The
192 drift in the observables will be subtracted before computing the
193 fluctuation properties.
194 -[no]fluc (no)
196 Calculate autocorrelation of energy fluctuations rather than
197 energy itself
198 -[no]orinst (no)
200 Analyse instantaneous orientation data
201 -[no]ovec (no)
203 Also plot the eigenvectors with -oten
204 -acflen <int> (-1)
206 Length of the ACF, default is half the number of frames
207 -[no]normalize (yes)
209 Normalize ACF
210 -P <enum> (0)
212 Order of Legendre polynomial for ACF (0 indicates none): 0, 1,
213 2, 3
214 -fitfn <enum> (none)
216 Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
217 -beginfit <real> (0)
219 Time where to begin the exponential fit of the correlation func‐
220 tion
221 -endfit <real> (-1)
223 Time where to end the exponential fit of the correlation func‐
224 tion, -1 is until the end
225
227 gmx(1)
228 More information about GROMACS is available at <‐
230 http://www.gromacs.org/>.
231
233 2019, GROMACS development team
2342018.7 May 29, 2019 GMX-ENERGY(1)