1GMX-ENERGY(1)                       GROMACS                      GMX-ENERGY(1)
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NAME

6       gmx-energy - Writes energies to xvg files and display averages
7

SYNOPSIS

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

DESCRIPTION

22       gmx  energy extracts energy components from an energy file. The user is
23       prompted to interactively select the desired energy terms.
24
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 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.
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39       The term fluctuation gives the RMSD around the least-squares fit.
40
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:
44
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                 └───────────────────────────┴─────────────────────┘
62
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
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
78       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
84          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
89       When a second energy file is specified (-f2), a free energy  difference
90       is calculated:
91
92          dF = -kT
93          ln(<exp(-(E_B-E_A) /
94          kT)>_A),
95
96       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.
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OPTIONS

103       Options to specify input files:
104
105       -f [<.edr>] (ener.edr)
106              Energy file
107
108       -f2 [<.edr>] (ener.edr) (Optional)
109              Energy file
110
111       -s [<.tpr>] (topol.tpr) (Optional)
112              Portable xdr run input file
113
114       Options to specify output files:
115
116       -o [<.xvg>] (energy.xvg)
117              xvgr/xmgr file
118
119       -viol [<.xvg>] (violaver.xvg) (Optional)
120              xvgr/xmgr file
121
122       -pairs [<.xvg>] (pairs.xvg) (Optional)
123              xvgr/xmgr file
124
125       -corr [<.xvg>] (enecorr.xvg) (Optional)
126              xvgr/xmgr file
127
128       -vis [<.xvg>] (visco.xvg) (Optional)
129              xvgr/xmgr file
130
131       -evisco [<.xvg>] (evisco.xvg) (Optional)
132              xvgr/xmgr file
133
134       -eviscoi [<.xvg>] (eviscoi.xvg) (Optional)
135              xvgr/xmgr file
136
137       -ravg [<.xvg>] (runavgdf.xvg) (Optional)
138              xvgr/xmgr file
139
140       -odh [<.xvg>] (dhdl.xvg) (Optional)
141              xvgr/xmgr file
142
143       Other options:
144
145       -b <time> (0)
146              Time of first frame to read from trajectory (default unit ps)
147
148       -e <time> (0)
149              Time of last frame to read from trajectory (default unit ps)
150
151       -[no]w (no)
152              View output .xvg, .xpm, .eps and .pdb files
153
154       -xvg <enum> (xmgrace)
155              xvg plot formatting: xmgrace, xmgr, none
156
157       -[no]fee (no)
158              Do a free energy estimate
159
160       -fetemp <real> (300)
161              Reference temperature for free energy calculation
162
163       -zero <real> (0)
164              Subtract a zero-point energy
165
166       -[no]sum (no)
167              Sum the energy terms selected rather than display them all
168
169       -[no]dp (no)
170              Print energies in high precision
171
172       -nbmin <int> (5)
173              Minimum number of blocks for error estimate
174
175       -nbmax <int> (5)
176              Maximum number of blocks for error estimate
177
178       -[no]mutot (no)
179              Compute the total dipole moment from the components
180
181       -[no]aver (no)
182              Also  print  the  exact  average  and  rmsd stored in the energy
183              frames (only when 1 term is requested)
184
185       -nmol <int> (1)
186              Number of molecules in your sample: the energies are divided  by
187              this number
188
189       -[no]fluct_props (no)
190              Compute  properties  based on energy fluctuations, like heat ca‐
191              pacity
192
193       -[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
198       -[no]fluc (no)
199              Calculate autocorrelation of energy fluctuations rather than en‐
200              ergy itself
201
202       -[no]orinst (no)
203              Analyse instantaneous orientation data
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205       -[no]ovec (no)
206              Also plot the eigenvectors with -oten
207
208       -acflen <int> (-1)
209              Length of the ACF, default is half the number of frames
210
211       -[no]normalize (yes)
212              Normalize ACF
213
214       -P <enum> (0)
215              Order  of  Legendre polynomial for ACF (0 indicates none): 0, 1,
216              2, 3
217
218       -fitfn <enum> (none)
219              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
220
221       -beginfit <real> (0)
222              Time where to begin the exponential fit of the correlation func‐
223              tion
224
225       -endfit <real> (-1)
226              Time  where  to end the exponential fit of the correlation func‐
227              tion, -1 is until the end
228

SEE ALSO

230       gmx(1)
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232       More    information    about    GROMACS    is    available    at     <‐
233       http://www.gromacs.org/>.
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236       2022, GROMACS development team
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2412022.3                           Sep 02, 2022                    GMX-ENERGY(1)
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