1 .TH g_tcaf 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
3 g_tcaf - calculates viscosities of liquids
9 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
11 .BI "\-ot" " transcur.xvg "
12 .BI "\-oa" " tcaf_all.xvg "
13 .BI "\-o" " tcaf.xvg "
14 .BI "\-of" " tcaf_fit.xvg "
15 .BI "\-oc" " tcaf_cub.xvg "
16 .BI "\-ov" " visc_k.xvg "
18 .BI "\-[no]version" ""
28 .BI "\-acflen" " int "
29 .BI "\-[no]normalize" ""
31 .BI "\-fitfn" " enum "
32 .BI "\-ncskip" " int "
33 .BI "\-beginfit" " real "
34 .BI "\-endfit" " real "
36 \&g_tcaf computes tranverse current autocorrelations.
37 \&These are used to estimate the shear viscosity eta.
38 \&For details see: Palmer, JCP 49 (1994) pp 359\-366.
41 \&Transverse currents are calculated using the
42 \&k\-vectors (1,0,0) and (2,0,0) each also in the y\- and z\-direction,
43 \&(1,1,0) and (1,\-1,0) each also in the 2 other planes (these vectors
44 \&are not independent) and (1,1,1) and the 3 other box diagonals (also
45 \¬ independent). For each k\-vector the sine and cosine are used, in
46 \&combination with the velocity in 2 perpendicular directions. This gives
47 \&a total of 16*2*2=64 transverse currents. One autocorrelation is
48 \&calculated fitted for each k\-vector, which gives 16 tcaf's. Each of
49 \&these tcaf's is fitted to f(t) = exp(\-v)(cosh(Wv) + 1/W sinh(Wv)),
50 \&v = \-t/(2 tau), W = sqrt(1 \- 4 tau eta/rho k2), which gives 16 tau's
51 \&and eta's. The fit weights decay with time as exp(\-t/wt), the tcaf and
52 \&fit are calculated up to time 5*wt.
53 \&The eta's should be fitted to 1 \- a eta(k) k2, from which
54 \&one can estimate the shear viscosity at k=0.
57 \&When the box is cubic, one can use the option \fB \-oc\fR, which
58 \&averages the tcaf's over all k\-vectors with the same length.
59 \&This results in more accurate tcaf's.
60 \&Both the cubic tcaf's and fits are written to \fB \-oc\fR
61 \&The cubic eta estimates are also written to \fB \-ov\fR.
64 \&With option \fB \-mol\fR the transverse current is determined of
65 \&molecules instead of atoms. In this case the index group should
66 \&consist of molecule numbers instead of atom numbers.
69 \&The k\-dependent viscosities in the \fB \-ov\fR file should be
70 \&fitted to eta(k) = eta0 (1 \- a k2) to obtain the viscosity at
71 \&infinite wavelength.
74 \&NOTE: make sure you write coordinates and velocities often enough.
75 \&The initial, non\-exponential, part of the autocorrelation function
76 \&is very important for obtaining a good fit.
80 Full precision trajectory: trr trj cpt
82 .BI "\-s" " topol.tpr"
84 Structure+mass(db): tpr tpb tpa gro g96 pdb
86 .BI "\-n" " index.ndx"
90 .BI "\-ot" " transcur.xvg"
94 .BI "\-oa" " tcaf_all.xvg"
102 .BI "\-of" " tcaf_fit.xvg"
106 .BI "\-oc" " tcaf_cub.xvg"
110 .BI "\-ov" " visc_k.xvg"
116 Print help info and quit
118 .BI "\-[no]version" "no "
119 Print version info and quit
121 .BI "\-nice" " int" " 19"
124 .BI "\-b" " time" " 0 "
125 First frame (ps) to read from trajectory
127 .BI "\-e" " time" " 0 "
128 Last frame (ps) to read from trajectory
130 .BI "\-dt" " time" " 0 "
131 Only use frame when t MOD dt = first time (ps)
134 View output xvg, xpm, eps and pdb files
136 .BI "\-xvg" " enum" " xmgrace"
137 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
139 .BI "\-[no]mol" "no "
140 Calculate tcaf of molecules
142 .BI "\-[no]k34" "no "
143 Also use k=(3,0,0) and k=(4,0,0)
145 .BI "\-wt" " real" " 5 "
146 Exponential decay time for the TCAF fit weights
148 .BI "\-acflen" " int" " \-1"
149 Length of the ACF, default is half the number of frames
151 .BI "\-[no]normalize" "yes "
154 .BI "\-P" " enum" " 0"
155 Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR
157 .BI "\-fitfn" " enum" " none"
158 Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR or \fB exp9\fR
160 .BI "\-ncskip" " int" " 0"
161 Skip N points in the output file of correlation functions
163 .BI "\-beginfit" " real" " 0 "
164 Time where to begin the exponential fit of the correlation function
166 .BI "\-endfit" " real" " \-1 "
167 Time where to end the exponential fit of the correlation function, \-1 is until the end
172 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.