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

6       gmx-energy - Writes energies to xvg files and display averages
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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.
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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:
87
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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OPTIONS

97       Options to specify input files:
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99       -f [<.edr>] (ener.edr)
100              Energy file
101
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
115
116       -pairs [<.xvg>] (pairs.xvg) (Optional)
117              xvgr/xmgr file
118
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
130
131       -ravg [<.xvg>] (runavgdf.xvg) (Optional)
132              xvgr/xmgr file
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134       -odh [<.xvg>] (dhdl.xvg) (Optional)
135              xvgr/xmgr file
136
137       Other options:
138
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)
144
145       -[no]w (no)
146              View output .xvg, .xpm, .eps and .pdb files
147
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
159
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
171
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)
178
179       -nmol <int> (1)
180              Number of molecules in your sample: the energies are divided  by
181              this number
182
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
207
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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SEE ALSO

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       2019, GROMACS development team
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2352019.4                           Oct 02, 2019                    GMX-ENERGY(1)
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