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>]
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22 gmx energy extracts energy components from an energy file. The user is
23 prompted to interactively select the desired energy terms.
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25 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.
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39 The term fluctuation gives the RMSD around the least-squares fit.
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41 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:
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45 ┌───────────────────────────┬─────────────────────┐
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 └───────────────────────────┴─────────────────────┘
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63 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).
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67 Option -odh extracts and plots the free energy data (Hamiltoian differ‐
68 ences and/or the Hamiltonian derivative dhdl) from the ener.edr file.
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70 With -fee an estimate is calculated for the free-energy difference with
71 an ideal gas state:
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73 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)>)
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76 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:
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82 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
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85 When a second energy file is specified (-f2), a free energy difference
86 is calculated:
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88 dF = -kT ln(<exp(-(E_B-E_A)/kT)>_A) ,
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90 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.
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97 Options to specify input files:
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99 -f [<.edr>] (ener.edr)
100 Energy file
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102 -f2 [<.edr>] (ener.edr) (Optional)
103 Energy file
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105 -s [<.tpr>] (topol.tpr) (Optional)
106 Portable xdr run input file
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108 Options to specify output files:
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110 -o [<.xvg>] (energy.xvg)
111 xvgr/xmgr file
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113 -viol [<.xvg>] (violaver.xvg) (Optional)
114 xvgr/xmgr file
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116 -pairs [<.xvg>] (pairs.xvg) (Optional)
117 xvgr/xmgr file
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119 -corr [<.xvg>] (enecorr.xvg) (Optional)
120 xvgr/xmgr file
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122 -vis [<.xvg>] (visco.xvg) (Optional)
123 xvgr/xmgr file
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125 -evisco [<.xvg>] (evisco.xvg) (Optional)
126 xvgr/xmgr file
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128 -eviscoi [<.xvg>] (eviscoi.xvg) (Optional)
129 xvgr/xmgr file
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131 -ravg [<.xvg>] (runavgdf.xvg) (Optional)
132 xvgr/xmgr file
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134 -odh [<.xvg>] (dhdl.xvg) (Optional)
135 xvgr/xmgr file
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137 Other options:
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139 -b <time> (0)
140 Time of first frame to read from trajectory (default unit ps)
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142 -e <time> (0)
143 Time of last frame to read from trajectory (default unit ps)
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145 -[no]w (no)
146 View output .xvg, .xpm, .eps and .pdb files
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148 -xvg <enum> (xmgrace)
149 xvg plot formatting: xmgrace, xmgr, none
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151 -[no]fee (no)
152 Do a free energy estimate
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154 -fetemp <real> (300)
155 Reference temperature for free energy calculation
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157 -zero <real> (0)
158 Subtract a zero-point energy
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160 -[no]sum (no)
161 Sum the energy terms selected rather than display them all
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163 -[no]dp (no)
164 Print energies in high precision
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166 -nbmin <int> (5)
167 Minimum number of blocks for error estimate
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169 -nbmax <int> (5)
170 Maximum number of blocks for error estimate
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172 -[no]mutot (no)
173 Compute the total dipole moment from the components
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175 -[no]aver (no)
176 Also print the exact average and rmsd stored in the energy
177 frames (only when 1 term is requested)
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179 -nmol <int> (1)
180 Number of molecules in your sample: the energies are divided by
181 this number
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183 -[no]fluct_props (no)
184 Compute properties based on energy fluctuations, like heat
185 capacity
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187 -[no]driftcorr (no)
188 Useful only for calculations of fluctuation properties. The
189 drift in the observables will be subtracted before computing the
190 fluctuation properties.
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192 -[no]fluc (no)
193 Calculate autocorrelation of energy fluctuations rather than
194 energy itself
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196 -[no]orinst (no)
197 Analyse instantaneous orientation data
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199 -[no]ovec (no)
200 Also plot the eigenvectors with -oten
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202 -acflen <int> (-1)
203 Length of the ACF, default is half the number of frames
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205 -[no]normalize (yes)
206 Normalize ACF
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208 -P <enum> (0)
209 Order of Legendre polynomial for ACF (0 indicates none): 0, 1,
210 2, 3
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212 -fitfn <enum> (none)
213 Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
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215 -beginfit <real> (0)
216 Time where to begin the exponential fit of the correlation func‐
217 tion
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219 -endfit <real> (-1)
220 Time where to end the exponential fit of the correlation func‐
221 tion, -1 is until the end
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224 gmx(1)
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226 More information about GROMACS is available at <‐
227 http://www.gromacs.org/>.
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230 2020, GROMACS development team
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2352019.6 Feb 28, 2020 GMX-ENERGY(1)