[gmx-users] g_rmsf residue average
Byungchan Kim
bk385 at columbia.edu
Wed Dec 31 00:27:01 CET 2003
Hi again.
I carefully look at the g_rmsf.c file.
If I understand correctly, the sequence of some statements is wrong.
First, the program should calculate rmsf for each atom and then
calculate the average. But the code is like this
if (bRes) {
average_residues(rmsf,isize,index,w_rls,&top.atoms);
label = "Residue";
} else
label = "Atom";
for(i=0; i<isize; i++)
rmsf[i] = U[i][XX][XX] + U[i][YY][YY] + U[i][ZZ][ZZ];
It seems that the program calculate the average first and then calculate
rmsf for each atom.
Please let me know if I am wrong.
Thank you.
Byungchan Kim
On Tue, 30 Dec 2003, Byungchan Kim wrote:
> 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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