Dear Gromacs users
Here comes a simple console utility for viewing g_rms output
writen in awk + shell. Usage is
./RMSDview file.xvg
The script is:
!!!!!!!!!!!!begining of file!!!!!!!!!!!!
#!/bin/sh
egrep -v @ $1 | egrep -v "#" | awk '
BEGIN {
OFS = ""
ORS = ""
print "\t" " RMSD (nm)\n"
print "\t" " 0.0 0.1 0.2 0.3 0.4 0.5\n"
print "\t" " | | | | | | \n"
print "\t" " -------------------------------------------------- \n"
}
{OFS = ""
ORS = ""
printf "%3.2f", $1
print "\t|"
first[NR] = $2
second[NR] = $3
third[NR] = $4
fourth[NR] = $5
for (i=1; i<51; i++) {
j = ((i - 1) / 100)
k = (i / 100)
if ((fourth[NR] >= j) && (fourth[NR] < k)) {
print "4"}
else {
if ((third[NR] >= j) && (third[NR] < k)) {
print "3"}
else {
if ((second[NR] >= j) && (second[NR] < k)) {
print "2"}
else {
if ((first[NR] >= j) && (first[NR] < k)) {
print "1"}
else {
print " "}
}
}
}
}
print "|\n"}
END {
print "\t" " -------------------------------------------------- \n"
}
'
!!!!!!!!!!!!!!!!!end of file!!!!!!!!!!!!!!
The output looks like:
RMSD (nm)
0.0 0.1 0.2 0.3 0.4 0.5
| | | | | |
--------------------------------------------------
0.00 |3 |
2.00 | 3 1 2 |
4.00 | 3 2 1 |
6.00 | 2 3 1 |
8.00 | 3 12 |
10.00 | 3 21 |
12.00 | 2 3 1 |
14.00 | 3 2 1 |
16.00 | 2 3 1 |
18.00 | 32 1 |
20.00 | 2 3 1 |
22.00 | 3 2 1 |
24.00 | 3 21 |
26.00 | 3 2 1 |
28.00 | 23 1 |
30.00 | 23 1 |
32.00 | 2 3 1 |
34.00 | 3 1 |
36.00 | 2 3 |
38.00 | 2 3 1 |
40.00 | 2 3 1 |
42.00 | 2 3 1 |
44.00 | 2 3 1 |
46.00 | 3 1 |
48.00 | 2 3 |
50.00 | 2 3 1 |
52.00 | 3 1 |
54.00 | 32 1 |
56.00 | 23 1 |
58.00 | 2 3 1 |
60.00 | 2 3 1 |
62.00 | 32 1 |
64.00 | 2 3 1 |
66.00 | 2 3 1 |
68.00 | 3 2 1 |
70.00 | 3 2 1 |
72.00 | 2 31 |
74.00 | 2 3 |
76.00 | 2 3 1 |
78.00 | 2 3 1 |
80.00 | 2 3 1 |
82.00 | 2 3 1 |
84.00 | 2 3 1 |
86.00 | 2 3 |
88.00 | 23 1 |
90.00 | 2 13 |
92.00 | 2 3 1 |
94.00 | 23 1 |
96.00 | 3 2 1 |
98.00 | 2 3 1 |
100.00 | 2 3 1 |
102.00 | 2 3 1 |
104.00 | 23 1 |
106.00 | 2 3 1 |
108.00 | 2 3 1 |
110.00 | 3 1 |
112.00 | 2 3 1 |
114.00 | 2 3 1 |
116.00 | 3 1 |
118.00 | 3 21 |
120.00 | 3 1 |
122.00 | 2 3 1 |
124.00 | 23 1 |
126.00 | 2 3 1 |
128.00 | 2 3 1 |
130.00 | 3 1 |
132.00 | 2 3 1 |
134.00 | 3 2 1 |
136.00 | 3 21 |
138.00 | 3 2 1 |
140.00 | 3 2 1 |
142.00 | 3 2 1 |
144.00 | 3 2 1 |
146.00 | 3 2 1 |
148.00 | 3 2 1 |
150.00 | 2 3 1 |
152.00 | 3 2 1 |
154.00 | 3 2 1 |
156.00 | 3 2 1 |
158.00 | 3 2 1 |
160.00 | 32 1 |
162.00 | 3 2 1 |
164.00 | 3 2 1 |
166.00 | 3 2 1 |
168.00 | 2 3 1 |
170.00 | 3 2 1 |
172.00 | 3 2 1 |
174.00 | 32 1 |
176.00 | 32 1 |
178.00 | 2 3 1 |
180.00 | 32 1 |
182.00 | 2 3 1 |
184.00 | 2 3 1 |
186.00 | 3 1 |
188.00 | 2 3 1 |
190.00 | 3 12 |
192.00 | 3 2 |
194.00 | 3 1 |
196.00 | 3 1 |
198.00 | 2 3 1 |
200.00 | 2 3 1 |
--------------------------------------------------
It can be easilly costomized for your number of rows, RMSD range
or for other input (g_hbond etc.).
I hope it can help you.
Vojtech Spiwok