1GMX-CURRENT(1) GROMACS GMX-CURRENT(1)
2
6 gmx-current - Calculate dielectric constants and current autocorrela‐
7 tion function
8
10 gmx current [-s [<.tpr/.gro/...>]] [-n [<.ndx>]] [-f [<.xtc/.trr/...>]]
11 [-o [<.xvg>]] [-caf [<.xvg>]] [-dsp [<.xvg>]]
12 [-md [<.xvg>]] [-mj [<.xvg>]] [-mc [<.xvg>]] [-b <time>]
13 [-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>]
14 [-sh <int>] [-[no]nojump] [-eps <real>] [-bfit <real>]
15 [-efit <real>] [-bvit <real>] [-evit <real>]
16 [-temp <real>]
17
19 gmx current is a tool for calculating the current autocorrelation func‐
20 tion, the correlation of the rotational and translational dipole moment
21 of the system, and the resulting static dielectric constant. To obtain
22 a reasonable result, the index group has to be neutral. Furthermore,
23 the routine is capable of extracting the static conductivity from the
24 current autocorrelation function, if velocities are given. Addition‐
25 ally, an Einstein-Helfand fit can be used to obtain the static conduc‐
26 tivity.
27 The flag -caf is for the output of the current autocorrelation function
29 and -mc writes the correlation of the rotational and translational part
30 of the dipole moment in the corresponding file. However, this option is
31 only available for trajectories containing velocities. Options -sh and
32 -tr are responsible for the averaging and integration of the autocorre‐
33 lation functions. Since averaging proceeds by shifting the starting
34 point through the trajectory, the shift can be modified with -sh to
35 enable the choice of uncorrelated starting points. Towards the end,
36 statistical inaccuracy grows and integrating the correlation function
37 only yields reliable values until a certain point, depending on the
38 number of frames. The option -tr controls the region of the integral
39 taken into account for calculating the static dielectric constant.
40 Option -temp sets the temperature required for the computation of the
42 static dielectric constant.
43 Option -eps controls the dielectric constant of the surrounding medium
45 for simulations using a Reaction Field or dipole corrections of the
46 Ewald summation (-eps=0 corresponds to tin-foil boundary conditions).
47 -[no]nojump unfolds the coordinates to allow free diffusion. This is
49 required to get a continuous translational dipole moment, required for
50 the Einstein-Helfand fit. The results from the fit allow the determina‐
51 tion of the dielectric constant for system of charged molecules. How‐
52 ever, it is also possible to extract the dielectric constant from the
53 fluctuations of the total dipole moment in folded coordinates. But this
54 option has to be used with care, since only very short time spans ful‐
55 fill the approximation that the density of the molecules is approxi‐
56 mately constant and the averages are already converged. To be on the
57 safe side, the dielectric constant should be calculated with the help
58 of the Einstein-Helfand method for the translational part of the
59 dielectric constant.
60
62 Options to specify input files:
63 -s [<.tpr/.gro/…>] (topol.tpr)
65 Structure+mass(db): tpr gro g96 pdb brk ent
66 -n [<.ndx>] (index.ndx) (Optional)
68 Index file
69 -f [<.xtc/.trr/…>] (traj.xtc)
71 Trajectory: xtc trr cpt gro g96 pdb tng
72 Options to specify output files:
74 -o [<.xvg>] (current.xvg)
76 xvgr/xmgr file
77 -caf [<.xvg>] (caf.xvg) (Optional)
79 xvgr/xmgr file
80 -dsp [<.xvg>] (dsp.xvg)
82 xvgr/xmgr file
83 -md [<.xvg>] (md.xvg)
85 xvgr/xmgr file
86 -mj [<.xvg>] (mj.xvg)
88 xvgr/xmgr file
89 -mc [<.xvg>] (mc.xvg) (Optional)
91 xvgr/xmgr file
92 Other options:
94 -b <time> (0)
96 Time of first frame to read from trajectory (default unit ps)
97 -e <time> (0)
99 Time of last frame to read from trajectory (default unit ps)
100 -dt <time> (0)
102 Only use frame when t MOD dt = first time (default unit ps)
103 -[no]w (no)
105 View output .xvg, .xpm, .eps and .pdb files
106 -xvg <enum> (xmgrace)
108 xvg plot formatting: xmgrace, xmgr, none
109 -sh <int> (1000)
111 Shift of the frames for averaging the correlation functions and
112 the mean-square displacement.
113 -[no]nojump (yes)
115 Removes jumps of atoms across the box.
116 -eps <real> (0)
118 Dielectric constant of the surrounding medium. The value zero
119 corresponds to infinity (tin-foil boundary conditions).
120 -bfit <real> (100)
122 Begin of the fit of the straight line to the MSD of the transla‐
123 tional fraction of the dipole moment.
124 -efit <real> (400)
126 End of the fit of the straight line to the MSD of the transla‐
127 tional fraction of the dipole moment.
128 -bvit <real> (0.5)
130 Begin of the fit of the current autocorrelation function to
131 a*t^b.
132 -evit <real> (5)
134 End of the fit of the current autocorrelation function to a*t^b.
135 -temp <real> (300)
137 Temperature for calculating epsilon.
138
140 gmx(1)
141 More information about GROMACS is available at <‐
143 http://www.gromacs.org/>.
144
146 2019, GROMACS development team
1472018.7 May 29, 2019 GMX-CURRENT(1)