From: Olaf Lenz (olenz_at_fias.uni-frankfurt.de)
Date: Thu Oct 26 2006 - 07:28:52 CDT

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Hello!

Although VMD is not specifically made for coarse-grained and
hand-written simulations, it is already very useful for their visualisation.
However, to be able to visualise them, it is always necessary to
translate the structures, trajectories and configurations into one of
the file formats that VMD understands. These file formats were created
with a specific simulation application in mind, and do normally not
allow to specify all of VMDs features (like, for example, the VDW radii,
or the size of the periodic box).

I want to propose new simple structure, coordinate and trajectory file
formats (VSF, VCF and VTF) that are explicitly designed to give the user
maximal control over VMD, i.e. that allows the user to explicitly set
all the information that can be set in VMD file reader plugins, without
pressing the user into any schemes given by other formats.

Attached, you will find
1. "vtfplugin.c" - The source code of the molfile reader plugin for the
format. The plugin uses only standard C libraries and I've tried to use
only POSIX functions and features, therefore it should compile on all
platforms.
2. "vtf.html" - Description of the format.
3. "vtfplugin.html" - Short description of the plugin suitable for
http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/.
4. "colloid_pe.vtf" - An example VTF file that contains a trajectory of
a coarse-grained colloid-polyelectrolyte system simulated in the
NPT-ensemble (with fluctuating unitcell size).

The format is already used by the CVS version of the coarse-grained
MD simulation package ESPResSo (http://www.espresso.mpg.de/).

So far, the plugin does only read the format, but extending the plugin
to write the format should be easy. Also, the format can be simply
adapted to any new developments in VMD.

It would be nice to have corresponding formats for the other VMD file
types (volumetric data, rawgraphics data and qm data), and it should be
easy to write such files, but so far, I don't plan to.

I would be happy if the plugin would become part of VMD in one of the
future versions, and I hereby grant the VMD team the permission to do
so. If there are some issues about the copyright, please contact me.

Best regards

        Olaf Lenz
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unitcell 20.0 20.0 20.0
atom 0:4 radius 2.0 segid 0
atom 5:154 radius 0.5 segid 1
bond 6:5
bond 7:6
bond 8:7
bond 9:8
bond 10:9
bond 11:10
bond 12:11
bond 13:12
bond 14:13
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bond 50:49
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bond 112:111
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bond 114:113
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bond 116:115
bond 117:116
bond 118:117
bond 119:118
bond 120:119
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bond 132:131
bond 133:132
bond 134:133
bond 135:134
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bond 137:136
bond 138:137
bond 139:138
bond 140:139
bond 141:140
bond 142:141
bond 143:142
bond 144:143
bond 145:144
bond 146:145
bond 147:146
bond 148:147
bond 149:148
bond 150:149
bond 151:150
bond 152:151
bond 153:152
bond 154:153

timestep
unitcell 20.0 20.0 20.0
17.57862 18.65746 8.15962
10.09662 13.79396 12.44118
12.57676 9.7919 15.16204
1.8371 8.79524 8.53514
0.11098 11.45076 12.81512
13.972619052 17.6979417902 3.63438546827
14.1309362599 17.282127677 4.52994913711
14.1448117787 17.8362459053 5.36227146595
14.4469344893 18.2899561646 6.20064421615
14.4150478267 17.9134534058 5.27477764189
14.805877775 18.3052523848 4.44186377389
14.2031152504 18.1145454831 3.66706817725
14.3506114831 18.6534588944 4.49641562945
14.8330432139 18.9182130088 5.33137963111
14.5267390073 19.5280217749 6.06234543181
13.9927442132 18.8098717782 5.61612783682
14.1466907702 19.6298276751 6.16746510621
13.8982792424 18.7913672472 6.65251749877
13.9619617748 18.7885170176 5.65455136144
13.3482940572 18.7755856796 6.44400985495
13.9276569405 18.2999151434 7.10588309847
13.6067428681 19.2142672545 6.85895319929
13.5529217098 19.1985557411 5.86052622086
13.7543628331 18.98875837 4.90375742072
13.8927204672 18.4032011601 4.10502096917
13.2419722072 19.0366274824 3.68633517246
14.0370549619 18.7932711293 3.13079840632
13.2968155692 18.2753072674 3.55946970132
14.2470371411 18.5673666323 3.66800675255
14.4524532227 18.3899398915 4.63046401659
13.4983172551 18.0906775939 4.62230114358
13.5827710871 17.1486286406 4.94697223847
12.8022886903 16.9722998131 5.54676834782
12.5974127416 16.9415575067 6.52507339037
13.4500747368 17.4303014823 6.34042007099
4.7542242728 15.7540336697 12.3202905302
4.88302532941 15.9735354959 13.2873630385
5.08956621411 16.3520586575 12.3851097043
5.3235519733 17.3231212058 12.337274655
4.6141504736 17.380164162 13.0397670844
4.89638408029 17.1951044367 12.0984397825
4.44529097 17.3278795094 12.9809848442
3.72252586125 17.7581641406 12.440183833
3.16780248454 18.4627639481 11.9976670688
3.03020674515 19.0532501891 11.2024353971
2.56676679328 19.5824202415 10.4916594361
1.60477483227 19.3160980179 10.4312943787
1.31387861245 19.9914946701 11.1089511882
1.58363580805 19.8547134723 10.1557870054
1.17770039885 20.4837205236 9.49278883577
1.35336593271 19.5281030495 9.25627908243
1.27471435091 19.6574078933 10.2447598289
0.74891796177 19.2335471721 9.50727745876
0.992066273959 19.5628268461 10.4196665175
0.999732802238 20.5594609681 10.3380475782
1.43979277076 21.2597678553 10.900112955
1.04296664517 21.2416014968 9.98239894207
0.717943979532 22.1545761672 9.73574631608
0.907572007264 22.2839505049 10.7090414881
1.20658881116 21.4186571579 11.1113552644
0.683691160134 22.157904538 10.6869835435
1.22232715465 21.42521282 11.1029572348
1.52129778178 21.8013083894 11.9799798609
1.70582199186 20.907538018 11.5711701998
2.55761712335 20.6454497105 12.0247721983
18.399603394 16.271745477 15.2096798249
18.3646422523 15.9446066173 16.1540091557
18.483953596 15.92304385 15.1613864427
18.0418111068 15.7877126508 14.2747097903
18.560322492 15.8169232242 15.1292814292
19.497599829 16.1492504718 15.0240683401
20.3758324754 16.0376739154 15.4891039202
19.7847587124 16.534955352 16.1241968107
19.1316296653 17.2837684495 16.2368972669
20.0456852265 17.6497603674 16.0621049701
19.8940380668 18.3276731755 15.3427737783
20.8568556668 18.1831382718 15.5710103457
21.3043144036 19.0563371034 15.7641540211
20.7915783611 18.2158605827 15.9393709406
20.1313929398 17.63564542 16.4163463848
20.6141939992 16.7606897544 16.3795262772
20.2943467327 16.9117698654 17.3148724838
21.1666667452 17.2007197215 17.7092907598
21.072750331 16.2436329865 17.9834525529
20.7939796553 16.3786871885 18.9342665583
19.8647992864 16.3423080092 19.3020985817
19.839555108 16.3436667635 18.3024181901
18.9166066154 16.4726818221 17.9397596803
18.9367957459 15.800884915 17.1992994757
19.2534101537 16.0285523759 18.1201267364
19.4166357216 15.7562650104 19.0683972698
19.011761011 16.3677811128 18.388599855
19.0106459625 16.4063506118 19.3878551529
18.4889181733 15.7396826515 18.8555451449
18.35435185 16.7074331672 18.6425877689
11.1240866553 12.4096050451 19.0026605218
10.927080614 12.6727069382 18.0582209983
11.2228216355 11.7740706599 17.7341992588
11.7347382598 12.5976271825 17.489871561
11.7798568665 12.5980786573 16.4908900259
12.7676623978 12.7186154748 16.3923450716
13.0689483741 12.2296080837 15.5737496086
13.1003449922 11.9251224207 16.5257489434
12.9605172314 12.3346654266 17.4272602986
12.3274131898 11.643884472 17.0779739617
12.2232102504 10.7064302576 17.4101205308
12.8829874509 10.2378085934 17.9975622569
13.170570938 10.5258610459 17.0841502346
13.5126110751 11.2569502985 16.4937969087
14.0610977927 11.0489248431 17.3036658676
13.9213084561 10.2544215768 16.7127145149
13.5792325565 11.0842603798 17.1535678236
13.6330000079 10.978599638 18.1465153896
13.0573984852 11.5815644579 18.6988887354
13.7461474943 11.2562724019 18.0509613622
13.4024235648 11.5855731363 18.9304014606
13.7751604384 11.021726995 18.1934179113
12.8780286771 11.2252519784 17.8013309514
13.5388386903 11.9703218129 17.7107712017
13.1849400426 11.7700735102 16.797175906
12.57301518 12.3067779014 17.3781202742
12.5533564853 11.9486039756 16.4446723781
13.3814671072 12.0042231517 17.0024710024
13.3567207606 12.0357083383 18.0016688313
13.1888067401 12.5770312437 17.1777911742
15.4344689918 4.11655049963 18.8159984624
15.3680694602 4.07898109191 19.8130840364
16.1846044909 3.77608033597 20.3045325847
16.3961743466 2.81526984139 20.1254197999
15.6665715525 3.42997611631 20.4251129071
16.1029099342 2.92703165468 19.6790192902
15.3889917705 2.43466712831 20.176912882
15.4047689153 2.42633226572 21.1767536752
15.1335096972 2.83528423987 20.3054461982
14.6934447281 3.45828967995 19.6587569029
14.1416348994 3.52707580848 18.8276285244
14.0180430378 3.19832777 17.8913327491
14.8387884203 2.64285463677 17.7578164001
14.5441828152 2.95266837619 18.6618202632
14.9050885529 2.7871393273 17.7440255244
14.3477432661 3.22310811932 17.0374157002
14.348258531 3.22590694474 18.0374116507
13.9654344642 2.81612183128 17.2094491548
13.0813486306 2.56903185781 17.6061086862
12.6890535193 1.9453797821 16.9299706573
12.606992329 1.56797445688 17.8523757644
13.0171530998 2.26970155824 18.4349109284
13.1238451822 1.91008051832 17.50793223
13.1159217708 1.2684052417 18.2748677286
13.1744070187 0.448492158916 17.7053749609
12.9134955169 1.04297055042 18.4659803975
12.600740267 0.161505121746 18.1121402476
13.3486821506 0.335006519 17.4714529574
13.5981905577 -0.621660381989 17.3213396823
13.6323065938 -1.20859344173 18.1302560435

timestep
unitcell 20.0569476941 20.0569476941 20.0569476941
17.5976319443 18.7392561377 8.17751154587
10.1845234283 13.8127066688 12.4820162638
12.3413468592 9.51919708445 14.7241359174
1.85274638126 8.77282871606 8.60513103356
0.0865123313813 11.4029159171 12.8714519695
13.7300294347 17.3384348764 3.52121176666
14.4107885734 17.2462038456 4.39426402659
14.0765875363 17.5621729962 5.54292540904
14.7057762764 18.0797981652 6.335104973
15.1485429111 17.7334905794 5.33022257621
15.4866017851 18.1510714748 4.32547119106
14.7115151798 17.9798256318 3.62188868776
14.6365764962 19.390402555 4.53100675805
15.3839719272 18.9808218652 5.29207812324
15.0299908761 19.6009846132 6.21719993242
14.2962959858 19.1879239378 5.5377262105
13.987699533 20.0650177267 6.30350728732
14.1830045725 18.9977619045 6.66855559306
13.5007660384 18.4626826547 5.79134730926
12.9760515586 18.6482337746 6.67382601276
13.8683069867 18.2103059899 7.31941791622
13.3874572602 19.579725846 7.11925060012
13.231382212 19.5223356306 5.82991868351
13.462883571 19.293900926 4.78849359659
13.7265245374 18.5563120002 3.98850827908
13.1456113459 19.3996866349 3.60684305281
13.8318245622 18.9083180558 2.77611313587
13.0515576417 18.2157406234 3.25134872606
14.5768949239 19.0174226983 3.5276970661
14.4338899173 18.2963648448 4.72246788753
13.2503455328 17.9828514243 4.81192482821
13.4963473387 16.8935916179 4.88952235918
12.6663731356 16.9776687655 5.59229559396
12.5714557714 16.9505050428 6.66308755833
13.528677925 17.4185987622 6.479210923
4.58995716169 15.6044900357 12.3897416368
4.91549490687 16.0224774827 13.3776149985
5.29811520393 16.4485979402 12.41387953
5.61901003335 17.4857835339 12.3573148206
4.95701763307 17.730293956 13.1867346977
4.6061162846 17.2368244234 11.9653093986
4.16686018246 16.9804144544 13.0685629333
3.81706006383 17.7967529491 12.4412653466
3.04698389465 18.5044827444 12.1800436464
3.09126731684 19.0162139901 11.2279709542
2.67667912719 19.6479547423 10.4783655572
1.80219306501 18.9890023893 10.7008634725
1.40465514744 19.9636214137 11.2111642496
2.01545372263 20.3588949103 10.025480963
1.22066135239 20.512333527 9.28918740763
1.52111613438 19.4754527694 8.99605315087
1.24697895496 19.5941338808 10.0412502036
0.419370579988 19.1208871534 9.51230731291
0.40718584836 19.5012013704 10.7312505953
0.780075170937 20.5772005932 10.4603100216
2.0152946996 21.2680976396 10.5920086388
1.17033618489 21.4239291578 9.8992043169
0.667708769893 22.4059156053 9.6744511681
1.1154686763 22.796610645 10.6942135196
0.507003861913 21.2321208449 11.4447981995
0.277905650677 22.0565109369 10.7694466546
1.31234354246 21.840136223 11.1549871213
1.58943530713 21.9282468252 12.1995358533
1.7450982174 20.9394306041 11.7834452625
2.74366985198 20.7267608642 12.0788788394
18.3096221184 16.9723324061 15.3498622673
18.3042507944 16.0238796376 16.3009454337
18.2222629551 15.8971022723 15.2529980038
18.0863692332 15.8085882419 14.1940261254
18.972260869 15.1633251679 15.0532225657
19.5543481193 16.1997964225 15.0020740729
20.5377671062 16.0650427301 15.546825844
19.6995991007 16.507360414 16.1234743724
19.1016400236 17.3783239104 16.3190762555
20.0414108747 17.5546142163 15.7955750559
19.955812614 18.4869995684 15.2615723265
21.0283488437 18.2413806262 15.2488772758
21.4456628038 19.1751535655 15.738433405
20.9227968045 18.4446929626 16.3603083339
20.1524149951 17.8566654177 16.8430959288
20.75764609 16.8738660404 16.4140850238
20.3179319486 16.8822468123 17.3847366401
21.2235336111 17.3594621113 17.8708522804
21.1995114115 16.2673839551 17.988960495
21.0475810411 16.4698791834 19.0517682811
20.0067072901 16.5455529773 19.4506128499
20.1454467648 16.4753617133 18.3450647929
18.8649451035 16.7172684946 17.5822980485
18.9935307864 15.733958984 17.0761616057
19.4874198626 15.5978359759 18.0555173226
19.4957544459 15.6124408939 19.1476839424
19.1227459524 16.476235717 18.6445236439
18.8935781764 16.6108571544 19.6741306361
18.3918816087 15.7127686273 18.9445120167
18.0880163134 16.9059121262 18.7258292164
11.1500282902 12.462417974 19.1786751029
10.7343603395 12.7192757761 18.196456579
11.2242231964 11.7882035217 17.8637254545
11.5924830108 12.8864462131 17.5169357147
11.627597537 12.7836167658 16.4433144033
12.6960438886 12.9553614541 16.3478678967
13.0883518969 12.5098360054 15.107289351
13.3583338372 12.1220030602 16.0720434901
12.8633648678 12.899852333 17.5859489169
11.8937605159 11.4316383107 16.9843391861
11.9619824667 10.4692536196 17.5200078632
12.6089833113 9.91841266051 18.1719582173
13.021065096 10.2822512959 17.1440342475
13.8243371586 11.13733594 16.2837212834
14.7753260155 11.213184031 17.1686477286
14.0979355771 10.2038905402 16.8083049818
13.7669172273 11.0043943156 17.4420394134
13.4005691089 10.5664186162 18.4359580732
12.7688986423 11.5630507349 18.9075597221
14.3504611016 11.5867901935 18.3753119109
13.7794766399 11.5843843296 19.2388083899
14.3803526099 10.6158110373 18.7678342785
12.7750991585 11.1596217505 17.9032038547
13.6975947893 12.051060745 17.6549881068
13.0029469262 11.6266887668 16.9796686612
12.2435855952 12.0766170684 17.7346778698
12.3471516213 11.937630614 16.17863184
14.100102553 12.2877517474 16.7674820335
13.3144786147 12.4859286571 18.4760083663
13.7080068489 13.2477976218 17.0693439332
15.4890890682 4.07378105904 18.8353271575
15.4244952337 4.28513642018 19.9034230334
16.5084223982 3.95110843459 20.3484544828
16.6379977575 2.84260373895 20.3841574604
15.6962451439 3.41633341542 20.7813445896
15.967541158 3.03929861215 19.5174145327
15.6344856354 2.16070062518 20.1261000036
15.558916664 2.3924868414 21.2536571472
14.7833392086 2.76272699808 20.5463758027
14.6725124666 3.48725703412 19.6824310102
13.9331979399 3.73275159978 18.946101999
13.6559042708 3.17654860217 18.0560610276
14.6750434237 2.24683066241 17.8858889308
14.7159977269 2.82825717523 18.7915451966
15.5086385561 3.01127754922 17.7142113524
14.6032788737 3.47538371919 16.9180762332
14.6322998882 3.66049626882 18.0249853568
13.9441992236 2.64061819225 17.1858593354
12.879588337 2.76074304156 17.4774386096
12.5876007456 1.92132072889 16.7766591967
12.4058309308 1.57674770877 17.8627750156
13.0140879824 2.34963994174 18.5437460715
13.4368445618 1.73126208222 17.4788192383
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
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timestep
unitcell 18.3807029954 18.3807029954 18.3807029954
14.3421298292 11.8332959466 -1.76787595238
-1.90597664265 15.4571419099 13.121102752
15.6288169141 0.234398574259 19.5418554465
-10.1902824672 5.27120090454 -0.238476360589
0.297564866291 10.0843190249 10.9272475764
17.2564072616 20.3901286378 -0.0954007534953
16.7029040639 21.5170871728 -0.215211140946
16.6039075571 22.1234596865 0.774343079396
17.6964379014 22.2970029272 1.26416223529
19.0567287726 23.3865430482 0.668193763516
19.5199128962 22.0633978616 -0.0209602912083
19.7556393732 21.7091890994 1.62965011488
19.25422098 21.1823478817 2.64861630079
18.4266747672 21.7406253718 4.16499277928
19.0629652553 20.730922268 5.48975502283
19.1589488131 20.2458707294 7.18085903293
17.8519439351 19.9982591271 7.82365658368
17.7086322829 18.4299365138 7.64220225563
16.7783774502 17.7131329841 8.35469221152
15.6129422257 18.0114052741 8.20848804662
14.8187273329 18.1436031745 8.93669101508
14.1702149866 17.2712174645 8.5706856398
13.6162903501 17.1566958294 7.17471953676
12.4778703751 17.5358672392 7.91531070869
10.8738842306 17.4400367975 8.26828715835
10.520275886 16.1799376155 7.84493823979
9.88425142578 15.0484885682 7.73908437477
8.25853445523 14.8834640786 7.6084119259
7.12937180058 15.451468083 6.88377629493
5.92460812887 14.7693551073 5.92993998719
6.59322535442 13.4759857056 6.05548848229
6.68846570294 11.8807027544 5.85900862636
5.87027096851 10.9412414815 4.91032819146
5.63238565725 9.79231499219 4.04209087236
5.79039023793 8.53424480289 4.13068193467
1.05268830967 8.50653785082 4.61535715515
1.80743366191 10.0092364495 4.31292614923
1.54302126984 10.921762525 5.3565260011
1.6650454591 11.0281753367 6.59864862264
2.31266453391 11.6992360396 7.67936717236
3.18407142742 11.1248860929 7.82596232224
3.00365012644 9.91525149272 7.89186584601
2.29559582111 10.8354264826 8.90274074953
1.67806678633 12.4466785968 9.20353859473
1.17897318268 13.7208774855 8.57385019878
1.07682673307 13.5605294211 9.90892532923
1.25799094659 13.8298823466 11.0471974657
0.237336896643 13.0069131732 11.6261064551
-0.210345968058 14.6104715453 11.5083645182
0.764202554107 15.1798359825 12.0188691108
0.30171827427 16.3845897023 11.3816903037
-0.553283387206 17.797364002 11.3628743545
0.153596299204 18.7567091958 11.3686934338
1.49248798439 18.9210762778 10.895085847
3.133661056 19.0538100221 11.105485957
3.56541246899 19.4959819103 9.6348188673
4.49615179365 19.0043581325 9.03421564429
5.66103508469 20.1728846125 8.18373357205
6.25515922045 20.8524600954 7.22034724995
6.45823745325 21.2288794699 5.97288734116
7.31807495639 22.1501671176 6.04313934633
7.79628316482 23.1155673848 7.44720928703
7.60590331939 24.2553565741 7.45932550063
7.85766010481 25.057454129 6.43064168585
8.8104702986 24.240819165 5.59228900493
14.4395679017 13.3800214419 11.504310175
14.8827230821 13.0282112633 12.9284544329
13.9534771219 12.8680402524 13.2607460418
13.590886583 13.4415455321 14.4470123144
14.3072765131 14.8635679043 14.9904091509
13.8372675415 16.2799225617 15.2316040196
13.2720543446 17.5569975582 15.4060421074
14.0324108627 18.6490399716 16.2968580659
14.4834282495 17.7264294538 17.1751511256
15.8952384106 17.4819222365 17.3198469845
16.8367342033 17.4224069644 16.8334605478
16.8355221437 16.0858075135 15.6013924833
17.7652240202 16.3778462084 16.5502471249
19.0633228897 15.5897377872 17.7241644361
18.7190870298 16.3306953867 19.1589953176
17.7464268983 15.8741916945 18.6299047031
16.5134496673 14.952912586 18.8067367514
16.5012100578 15.0499233907 17.4592093814
16.5171263603 14.013744325 16.3854472472
17.271651814 13.3796683545 15.9803527983
18.665616564 12.6665119864 16.2520279618
18.8899000554 11.4580525064 15.6249748075
18.287656803 10.8974122457 16.4674766523
18.3576663135 9.49696665784 16.9278333427
18.6425944734 8.1236291152 17.197257723
17.3942357052 7.17775476208 17.2384021137
16.0246842757 7.14250578207 16.5100392204
15.5949592939 7.30584467934 15.5312863156
15.6827884996 7.18372934623 14.0481563372
16.7619822216 7.11128286323 12.8479601549
10.7580646019 8.55796452879 11.9285619258
10.4857311422 9.40306397801 13.3159292153
10.1671232408 9.89663655358 14.3494580872
8.87348135212 10.5094697665 13.7929171931
7.6620965634 10.2118199184 13.0551201627
7.06883408667 9.62374066455 14.05367385
6.13730528781 8.73988965573 13.7637340392
6.96396074086 7.91121167702 14.4094280263
7.39078099211 6.50664013956 14.9473139525
6.79930700935 7.36840669677 15.3596491057
7.87460341229 7.76462511557 16.3931977472
8.952315188 8.42667688757 16.410224079
9.69948162795 7.95072466772 17.3414937949
9.32859574343 8.8074705138 18.3893189179
10.5847537981 7.83038616677 18.85377583
11.565364865 8.2781123897 19.4074820252
12.2743356091 9.17562282323 19.7223979525
12.9673490811 10.1322714638 20.5366136615
13.1760555583 10.2517905594 21.6802716284
12.8171637834 11.1667045553 22.0932866178
13.2971399282 11.8425617403 23.4239725752
13.5482257617 11.4219938759 24.3518723931
14.6352287899 12.5935504784 24.3651681879
14.4104615808 13.0960595083 23.0830864845
13.449133132 12.4964512656 22.4122997297
12.3320900609 13.4200233496 22.2677678679
12.1102550212 13.3934571069 20.9425526595
12.9986193499 14.066537961 19.4449218375
12.1939197248 13.6108648637 18.3108057845
10.9523943901 13.9295011602 17.5838127843
15.7815298969 5.78987697286 22.0291086968
14.1818390665 5.82164607408 22.4272761276
13.2922440451 5.96031928026 23.4294313466
12.7824860398 5.42923726079 22.7729221388
11.8507407231 5.93954253226 22.8401478384
11.0874616297 4.68287904098 21.72505883
11.0752180138 3.75335650743 20.6334783463
11.6812353329 4.14964353995 19.3175662042
10.9587817618 3.31653415951 19.5499645241
12.1603102832 2.79276245063 18.6735662242
12.9686071382 2.40799334729 17.3528287091
13.1932059973 2.62137711013 15.9846272369
11.7011175823 2.19877765955 15.1429709517
12.2629753753 3.16462179897 14.5829899043
11.7702616556 3.92702072153 15.1751791565
10.8993689874 3.56969762046 15.9190160361
9.63737285557 3.99042549453 15.6250060218
8.65632365119 3.59926467224 15.2437483261
7.20010199384 3.02852567368 15.5082884173
7.47409991449 2.9244915423 16.5682895548
6.4780921608 3.33944863564 17.1627434935
5.48628246562 3.20572184765 17.9003131958
5.1932876646 2.51939497975 18.8268418265
5.33158954563 1.42788102071 18.9576997109
4.60417669131 1.02409853172 19.8309564188
4.2301250156 2.86000212993 19.910015246
4.8428675569 4.2373726707 19.2684126993
6.16186876245 4.96101223894 20.1267808596
6.07437147368 6.5489086209 20.7475874609
6.80013688225 7.11077240921 21.2880364592


VMD trajectory/structure/coordinate format

VMD trajectory/structure/coordinate format

The VMD trajectory/structure/coordinate format was designed for people using their own hand-written simulation codes and coarse-grained simulations that want to visualize their simulations using VMD. In VTF, VSF and VTF files, it is possible to specify all properties that are used by the VMD viewer.

Basic file format

  • The basic unit of a file is a line.
  • A block consists of an arbitrary number of lines, up to a line starting a new block.
  • Files consist of structure and timestep blocks.
  • VSF files only contain a structure block.
  • VCF files only contain timestep blocks.
  • VTF files start with a structure block and contain an arbitrary number of timestep blocks afterwards.
  • Lines ending with the character \ are continuation lines, i.e. the line is concatenated with the next line to form a single line.
  • Comment lines starting with # and lines containing only whitespace characters are ignored.
  • Leading whitespace characters in a line are ignored.

Structure blocks

Structure blocks describe the structure of a simulated system, i.e. the characteristics of the atoms, the bonds, and the unitcell size. Structure blocks consist of atom, bond and unitcell lines. Each line is identified by the first non-whitespace character.

Atom lines

Atom lines define atoms and their properties.
Syntax
[a[tom]] aid-specifier[,aid-specifier...] [options...]
    
Options
n[ame] char[16]       - atom name
t[ype] char[16]       - atom type
resid int             - residue id
res[name] char[8]     - residue name
r[adius] float        - VDW radius
s[egid] char[8]       - segment id
c[hain] char[2]       - chain id
charge|q float        - charge
a[tomicnumber] int    - atomic number
altloc char[2]        - PDB alternative location
i[nsertion] char[]    - PDB insertion
o[ccupancy] float     - occupancy
b[factor] float       - b-factor
m[ass] float          - mass
    
Example
# Specify 4 coarse-grained lipids with 7 beads each
atom 0,7,14,21 name HEAD resname LIPID radius 1.1
atom 1:2,8:13,15:20,22:27 name TAIL resname LIPID radius 1.0
atom 0:6 resid 0 segid UPPER
atom 7:13 resid 1 segid UPPER
# in fact, 'a' is enough to identify an atom line
a 14:20 resid 2 segid LOWER
# or even no keyword at all
21:27 resid 3 segid LOWER
    
  • The line starts with an aid-specifier or the keyword a[tom].
  • An aid-specifier specifies, which atoms the line refers to:
    • default refers to the default atom that is used as a template for new atoms.
    • A single atom id specifies a single atom.
    • A range specifier from:to denotes a range of atoms.
    • Whenever an atom id is used that is greater than the greatest atom id so far, all atoms up to this new greatest id are made copies of the default atom.
  • The options can be used to specify the different properties of the atoms.

Bond lines

Bond lines define bonds between atoms.
Syntax
 b[ond] bond-specifier[,bond-specifier...]
    
Example
# Specify a ring of 6 atoms
bond 0::5,5:0
    
  • The line starts with the keyword b[ond].
  • A bond-specifier defines one or more bonds:
    • from:to defines a bond between atoms from and to
    • from::to defines, that the atoms between from and to are a chain with bonds between two adjacent atoms

Unitcell/PBC lines

Unitcell lines define the size of the unitcell (or periodic boundary conditions) of the system.
Syntax
p[bc]|u[nitcell] a b c [alpha beta gamma]
    
Example
unitcell 10.0 10.0 10.0 90 90 90
    
  • The line starts with one of the keywords u[nitcell] or p[bc].
  • a,b and c define the dimensions of the unitcell in x,y and z directions.
  • alpha, beta and gamma define the angles of the unitcell as defined in the VMD user's guide.
  • If the angles are omitted, the unitcell is assumed to be rectangular.

Timestep/Coordinates blocks

Timestep/Coordinate blocks describe the positions of the atoms in a simulated system, as well as the size of the unitcell in a given timestep in a simulation where the unitcell size changes. A timestep/coordinate block starts with a timestep line. Depending on the timestep line, the following lines are either unitcell lines (as in the structure block) or coordinate definition lines in ordered or indexed format. If the unitcell data or the coordinates of some of the atoms are not specified in a timestep, they are taken from the previous timestep, if accessible.

Timestep/Coordinates line

A timestep/coordinate line defines a new set of coordinates that should be read into a new frame in VMD.
Syntax
t[imestep]|c[oordinates] [i[ndexed]|o[rdered]]|i[ndexed]|o[rdered]
    
Example
# several variants
timestep
coordinates
timestep indexed
ordered
# very short
t i
     
  • The line starts with one of the keywords t[imestep], c[oordinates], i[ndexed] or o[rdered].
  • The keyword o[rdered] specifies that the following coordinate definition lines are in ordered format.
  • The keyword i[ndexed] specifies that the following coordinate definition lines are in indexed format.
  • If no corresponding keyword is found, the following coordinate definition lines are assumend to be in ordered format.

Coordinate definition lines

Coordinate definition lines define the coordinates of a single atom in the system.
Syntax (ordered format)
x y z
    
Syntax (indexed format)
aid x y z
    
Example
timestep ordered
4.0 7.0 5.0
6.0 7.0 5.0
7.0 5.0 5.0
6.0 3.0 5.0
4.0 3.0 5.0
3.0 5.0 5.0

timestep indexed
0 5.0 7.0 5.0
     
  • In ordered format, the lines are associated with ascending atom ids.
  • In indexed format, the coordinates xy and z are associated with the atom id aid.
  • The first timestep in a multi-timestep file should be an ordered timestep, so that all atoms are defined.
  • The timestep in a single-timestep file should be an ordered timestep, so that all atoms are defined.

VMD trajectory/structure/coordinate format plugin

VMD trajectory/structure/coordinate format plugin

The plugin reads files written in the VMD trajectory/structure/coordinate format. The format was designed especially for VMD and is useful for hand-written simulation codes and coarse-grained simulations. It is currently used by the ESPResSo coarse-grained simulation package.

Notes:

Read-only
This plugin is used only to read files. VMD does not currently support writing this file type.