[gmx-users] g_rmsf residue average
Byungchan Kim
bk385 at columbia.edu
Tue Dec 30 23:47:01 CET 2003
Hi Folks.
I got strange output from g_rmsf. I picked only main chain atoms from
standard input. First I ran g_rmsf without -res and got
rmsf of each main chain atom. Then I ran the program with -res to get
average rmsf for each residue.
But the result of the residue averaged values look same as the value of
Oxygen of main chain of each residue, not averaged for main chain atoms. I
mean the -res doesn't seem to work. Are there any special treatments for
using g_rmsf and -res or did I make any mistake?
Thanks and Happy new year.
Byungchan Kim
P.S. commandline which I ran
1. g_rmsf -f 4pti.trj.xtc
2. g_rmsf -f 4pti.trj.xtc -res
output files
1.
# This file was created by g_rmsf
# which is part of G R O M A C S:
# Great Red Oystrich Makes All Chemists Sane
# All this happened at: Tue Dec 30 17:29:58 2003
#
@ title "RMS fluctuation"
@ xaxis label "Atom"
@ yaxis label "(nm)"
@TYPE xy
1 0.1294
2 0.1094
3 0.0912
4 0.0995
5 0.0780
6 0.0702
7 0.0633
8 0.0693
9 0.0623
10 0.0618
11 0.0535
12 0.0598
13 0.0502
14 0.0484
15 0.0457
16 0.0520
17 0.0447
18 0.0465
19 0.0457
20 0.0522
21 0.0457
22 0.0481
23 0.0493
24 0.0668
25 0.0466
26 0.0480
27 0.0462
28 0.0504
29 0.0470
30 0.0457
31 0.0416
32 0.0474
33 0.0415
34 0.0438
35 0.0418
36 0.0574
37 0.0412
38 0.0424
39 0.0358
40 0.0389
41 0.0376
42 0.0350
43 0.0363
44 0.0416
45 0.0438
46 0.0507
47 0.0528
48 0.0615
49 0.0580
50 0.0678
51 0.0664
52 0.0851
53 0.0587
54 0.0585
55 0.0585
56 0.0638
57 0.0683
58 0.0770
59 0.0743
60 0.1273
61 0.0745
62 0.0658
63 0.0641
64 0.0757
65 0.0627
66 0.0696
67 0.0627
68 0.0833
69 0.0508
70 0.0467
71 0.0422
72 0.0495
73 0.0429
74 0.0429
75 0.0416
76 0.0559
77 0.0368
78 0.0354
79 0.0352
80 0.0428
81 0.0370
82 0.0358
83 0.0345
84 0.0399
85 0.0358
86 0.0341
87 0.0336
88 0.0405
89 0.0339
90 0.0341
91 0.0356
92 0.0412
93 0.0406
94 0.0470
95 0.0505
96 0.0560
97 0.0617
98 0.0719
99 0.0756
100 0.0904
101 0.0749
102 0.0837
103 0.0845
104 0.1136
105 0.0730
106 0.0754
107 0.0729
108 0.0892
109 0.0640
110 0.0679
111 0.0619
112 0.0742
113 0.0541
114 0.0529
115 0.0437
116 0.0479
117 0.0430
118 0.0406
119 0.0421
120 0.0602
121 0.0386
122 0.0401
123 0.0387
124 0.0458
125 0.0425
126 0.0402
127 0.0388
128 0.0469
129 0.0372
130 0.0364
131 0.0342
132 0.0418
133 0.0365
134 0.0374
135 0.0349
136 0.0422
137 0.0384
138 0.0349
139 0.0336
140 0.0414
141 0.0354
142 0.0419
143 0.0441
144 0.0564
145 0.0433
146 0.0524
147 0.0540
148 0.0695
149 0.0486
150 0.0536
151 0.0518
152 0.0529
153 0.0584
154 0.0623
155 0.0574
156 0.0718
157 0.0552
158 0.0537
159 0.0541
160 0.0701
161 0.0471
162 0.0466
163 0.0455
164 0.0537
165 0.0459
166 0.0478
167 0.0435
168 0.0565
169 0.0387
170 0.0354
171 0.0342
172 0.0422
173 0.0366
174 0.0349
175 0.0375
176 0.0582
177 0.0359
178 0.0375
179 0.0383
180 0.0422
181 0.0440
182 0.0488
183 0.0527
184 0.0691
185 0.0497
186 0.0528
187 0.0498
188 0.0521
189 0.0523
190 0.0517
191 0.0494
192 0.0530
193 0.0534
194 0.0584
195 0.0549
196 0.0619
197 0.0533
198 0.0546
199 0.0470
200 0.0532
201 0.0419
202 0.0388
203 0.0397
204 0.0459
205 0.0435
206 0.0534
207 0.0567
208 0.0741
209 0.0535
210 0.0600
211 0.0576
212 0.0747
213 0.0485
214 0.0503
215 0.0487
216 0.0601
217 0.0455
218 0.0514
219 0.0678
220 0.1093
221 0.0640
222 0.0844
223 0.0885
224 0.1352
225 0.1126
226 0.1480
227 0.1805
228 0.2076
229 0.2326
230 0.2986
231 0.3422
232 0.3870
233 0.3786
2.
# This file was created by g_rmsf
# which is part of G R O M A C S:
# GRoups of Organic Molecules in ACtion for Science
# All this happened at: Tue Dec 30 17:23:35 2003
#
@ title "RMS fluctuation"
@ xaxis label "Residue"
@ yaxis label "(nm)"
@TYPE xy
1 0.0995
2 0.0693
3 0.0598
4 0.0520
5 0.0522
6 0.0668
7 0.0504
8 0.0474
9 0.0574
10 0.0389
11 0.0416
12 0.0615
13 0.0851
14 0.0638
15 0.1273
16 0.0757
17 0.0833
18 0.0495
19 0.0559
20 0.0428
21 0.0399
22 0.0405
23 0.0412
24 0.0560
25 0.0904
26 0.1136
27 0.0892
28 0.0742
29 0.0479
30 0.0602
31 0.0458
32 0.0469
33 0.0418
34 0.0422
35 0.0414
36 0.0564
37 0.0695
38 0.0529
39 0.0718
40 0.0701
41 0.0537
42 0.0565
43 0.0422
44 0.0582
45 0.0422
46 0.0691
47 0.0521
48 0.0530
49 0.0619
50 0.0532
51 0.0459
52 0.0741
53 0.0747
54 0.0601
55 0.1093
56 0.1352
57 0.2076
58 0.3786
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