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I'm new to VMD and I'm having some problems with displaying my polymer chain. Instead of just one bond, VMD draws multiple bonds. Why does this happen?

I'm creating the data with Lammps, below you can find the configuration file. The positions of each atom are generetad by a random walk.

# Specify number of atoms, bonds etc.
101 atoms
1 atom types
100 bonds
1 bond types

# Specify the dimensions of the simulation box
-500.0 500.0 xlo xhi
-500.0 500.0 ylo yhi
-500.0 500.0 zlo zhi

# No comments after this line!

Atoms

1 1 1 0.0 1.0 0.0
2 1 1 -0.7434993336043932 1.1973737373610782 0.6389462800032122
3 1 1 -0.4411948976553678 1.137570596339683 1.5902798767659445
4 1 1 -0.6329859116374574 1.143394721643678 2.571698384091013
5 1 1 -0.7016274442277435 1.5021302926345295 3.5026103724709694
6 1 1 -0.5443514760156292 1.5702089669785606 2.517405031477275
7 1 1 -0.5699191941809161 1.7003885169393316 1.5262443096163696
8 1 1 -1.3177350755405703 2.278804471390844 1.2003510890329563
9 1 1 -1.9977740218975115 1.8881888342630524 0.5798944382756367
10 1 1 -1.9319374150896353 2.08627847024584 -0.3980759280035424
11 1 1 -2.040305568769746 2.2015106556365667 -1.3854856133510385
12 1 1 -1.5958175497595544 2.1530871983399344 -0.49101058869141345
13 1 1 -1.6192876558657934 2.76194631148644 0.3019205145311884
14 1 1 -1.3422312299743706 3.2765219531221295 1.113370849368441
15 1 1 -2.181024985309463 3.8015202975945197 1.2575990515762703
16 1 1 -2.324236992177467 4.0230406461086625 0.2930167293854623
17 1 1 -2.730805712527504 4.3686486995612945 -0.5527119203726122
18 1 1 -1.8597726738426696 3.884999560889903 -0.6386476881406687
19 1 1 -2.255892784762997 3.037544231209013 -0.28522397371289987
20 1 1 -2.645888322818996 2.426064305276162 0.4032495410119348
21 1 1 -2.8111412810230143 3.277083105698413 0.9017056184477448
22 1 1 -2.1832603711837275 3.2535843704402443 1.6796602266998304
23 1 1 -2.1759625810777194 3.2884641985946117 0.6802953584722693
24 1 1 -2.685192387009965 2.700495667863554 0.05182259723263627
25 1 1 -2.937904635957768 2.8634421461362494 1.0055442361033655
26 1 1 -3.054065629991879 3.8538354706453704 0.9305263300223641
27 1 1 -2.554837947349212 3.9855623981159605 1.7869256162565308
28 1 1 -1.6415758191968515 3.7290099444914597 1.470487433001302
29 1 1 -1.8900749817872389 3.8052189230819775 2.436116946724897
30 1 1 -2.470739903718883 3.7661227632376364 1.6229135658148421
31 1 1 -2.6825374467370144 3.5115429556262314 2.5664870512032474
32 1 1 -1.780045547641019 3.296498831281347 2.9396685039187407
33 1 1 -1.0993076906782537 3.6770461834785997 2.313745439290665
34 1 1 -0.46195880715527926 3.7096758875111138 3.0836296533688397
35 1 1 -0.23841501293801096 3.672672252244473 2.1096384300798405
36 1 1 0.22877811484089797 3.6560029605085447 1.225640287508725
37 1 1 0.0682198250699318 3.734301163350403 2.2095561512986923
38 1 1 0.7230805203838258 3.926048293734055 1.4785359684564963
39 1 1 0.7684881429903485 4.252876337322301 2.4225283295132494
40 1 1 1.6113196542703498 4.49210929302465 1.9404467632826092
41 1 1 1.6398315199916553 4.657581062920609 2.926249059324056
42 1 1 1.2992558899263837 5.402093576553395 3.5004522962095983
43 1 1 1.8976509831206507 4.872438608347428 2.8992959712027324
44 1 1 1.971560715445052 5.2288808395108175 3.830685410326346
45 1 1 2.2016332012055035 5.24869273979793 4.803657218706744
46 1 1 1.89269657465061 6.199055974672456 4.840642115241796
47 1 1 1.8867800232249257 5.975229856368981 5.815253249584323
48 1 1 0.9802959416118275 5.939989229426677 5.394486440062979
49 1 1 1.047924037924727 5.669647029351694 4.434100301341833
50 1 1 1.065681202100049 4.672344116872239 4.505315355090657
51 1 1 1.9890223906338584 4.855672815127894 4.842704800617423
52 1 1 1.6981323684620444 4.380604923138391 4.012226930351436
53 1 1 1.5841075231538293 5.37359111660389 4.043479998030235
54 1 1 1.4194089647068764 4.616586260426731 3.4111683402461224
55 1 1 1.448631461286475 4.7192110548939015 4.405459141397489
56 1 1 1.0602825297012965 3.967251325525684 4.938133218807988
57 1 1 1.1665353695251628 3.9032366704083077 5.9304096208047135
58 1 1 0.6147436849584818 3.088703537358636 5.751351775382207
59 1 1 0.3894975765175991 3.43048570224102 6.6637382847084625
60 1 1 0.07289811630462367 3.452170914517765 7.612049696303496
61 1 1 0.20597075094139916 2.538021347220522 7.994962535630007
62 1 1 0.22023706250016878 1.7841668009752478 7.3380760953225215
63 1 1 0.30848510038867083 1.8413405224543755 8.33253245403368
64 1 1 0.40652915584533633 2.078520457537169 9.299038036833766
65 1 1 0.3418049476997458 2.814650573041588 8.625299786526291
66 1 1 1.174165755942365 2.8613112521175283 8.073033305622493
67 1 1 1.442960329852769 3.074362975392315 7.133693941896066
68 1 1 1.6864169820447585 3.466978437241009 8.020588500240407
69 1 1 2.2434929878955114 4.249342708614907 7.7420701515038095
70 1 1 2.067430021991088 4.02157894285066 8.699736846675897
71 1 1 1.943445379529309 4.050699677692111 7.707880107405593
72 1 1 1.6624284693755162 3.794748444773335 6.78293769699564
73 1 1 2.088879815897793 3.805001652998303 7.687390084228065
74 1 1 2.275671871180298 3.7529818076023047 8.668411319354153
75 1 1 2.356579533891821 3.2927396662140116 9.552510364373926
76 1 1 1.7742705290786691 2.7560175183894886 8.94189955629062
77 1 1 0.9444528173236891 2.2406800487846494 9.155978648401481
78 1 1 1.576588748426326 2.761354773732321 8.582130240361806
79 1 1 0.9428470651966604 2.6153768933219466 9.34177616931037
80 1 1 0.9257234064979147 2.32681969593226 8.384466645620472
81 1 1 0.7066303623606289 2.9396471968940485 9.143703559946683
82 1 1 1.0081424534717858 2.7935316251905995 8.201503634973458
83 1 1 0.215091367278472 2.3745267415388094 7.759344294731102
84 1 1 0.8363081855105148 2.914149076941315 8.327584912674244
85 1 1 0.344025941389587 3.7523816381838344 8.562157642112407
86 1 1 0.748192744185691 3.872513874138282 9.468919706494326
87 1 1 0.07077650273719471 3.7309390412545818 10.190767199054731
88 1 1 0.09958038174286468 3.7064596929845313 11.190052492683382
89 1 1 0.14518080386775778 3.391684978503032 10.241982094123696
90 1 1 0.40296951577248574 4.084394216445771 10.915553836169998
91 1 1 -0.001759231744961065 4.854355021503993 11.4088640829793
92 1 1 -0.36521564443071763 3.9227878338502715 11.399808092446126
93 1 1 -0.44182564884993936 3.049235462804667 10.91914483998814
94 1 1 0.42809855383893103 2.733950887333662 10.53989885379158
95 1 1 1.0255155357668442 2.9120441783129927 9.75799366170478
96 1 1 0.8925334926302557 2.908971670619831 10.749107346354375
97 1 1 1.5688207561101777 2.5114790617426905 11.369296965054078
98 1 1 0.6114222053258117 2.226292114441501 11.414644732860493
99 1 1 0.2194072585912204 2.206191188157631 10.494905512048852
100 1 1 -0.6863081538403157 1.7963549441711444 10.60313602899773
101 1 1 -0.9577783952771719 0.9208842115233563 11.002954618224594


Bonds

1 1 1 2
2 1 2 3
3 1 3 4
4 1 4 5
5 1 5 6
6 1 6 7
7 1 7 8
8 1 8 9
9 1 9 10
10 1 10 11
11 1 11 12
12 1 12 13
13 1 13 14
14 1 14 15
15 1 15 16
16 1 16 17
17 1 17 18
18 1 18 19
19 1 19 20
20 1 20 21
21 1 21 22
22 1 22 23
23 1 23 24
24 1 24 25
25 1 25 26
26 1 26 27
27 1 27 28
28 1 28 29
29 1 29 30
30 1 30 31
31 1 31 32
32 1 32 33
33 1 33 34
34 1 34 35
35 1 35 36
36 1 36 37
37 1 37 38
38 1 38 39
39 1 39 40
40 1 40 41
41 1 41 42
42 1 42 43
43 1 43 44
44 1 44 45
45 1 45 46
46 1 46 47
47 1 47 48
48 1 48 49
49 1 49 50
50 1 50 51
51 1 51 52
52 1 52 53
53 1 53 54
54 1 54 55
55 1 55 56
56 1 56 57
57 1 57 58
58 1 58 59
59 1 59 60
60 1 60 61
61 1 61 62
62 1 62 63
63 1 63 64
64 1 64 65
65 1 65 66
66 1 66 67
67 1 67 68
68 1 68 69
69 1 69 70
70 1 70 71
71 1 71 72
72 1 72 73
73 1 73 74
74 1 74 75
75 1 75 76
76 1 76 77
77 1 77 78
78 1 78 79
79 1 79 80
80 1 80 81
81 1 81 82
82 1 82 83
83 1 83 84
84 1 84 85
85 1 85 86
86 1 86 87
87 1 87 88
88 1 88 89
89 1 89 90
90 1 90 91
91 1 91 92
92 1 92 93
93 1 93 94
94 1 94 95
95 1 95 96
96 1 96 97
97 1 97 98
98 1 98 99
99 1 99 100
100 1 100 101

My polymer with multiple bonds from a single atom

Improve this question
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6
  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community
    Commented Dec 2, 2021 at 14:50
  • 2
    $\begingroup$ @jakobBoonen What files are you loading and how are you loading them in VMD? $\endgroup$
    – Vasista
    Commented Dec 4, 2021 at 7:22
  • 2
    $\begingroup$ If the input is a xyz file, VMD will draw bonds based on distances. That means that any atoms close enough to each other will be drawn with bonds. $\endgroup$
    – Hans Wurst
    Commented Dec 4, 2021 at 11:12
  • $\begingroup$ I edited the question with my configuration file from lampps. Is there a way to specify which atoms are bounded? $\endgroup$
    – Jakob Boonen
    Commented Dec 5, 2021 at 14:52
  • 1
    $\begingroup$ I'd recommend asking a new question! You can click on the edit history to get back the contents of your latest addition to the queation. $\endgroup$
    – Nike Dattani - No Free Time
    Commented Dec 13, 2021 at 19:24

1 Answer 1

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You have provided a LAMMPS data file as input to VMD and AFAIU, the default New Molecule option from VMD can't read this format. I am not sure how you are reading the given file, but I think the issue you are facing is due to the way you are reading the file in VMD.

You can use the TopoTools plugin (which is available by default in VMD) to read this file. As the file you provided is a LAMMPS data file with atom_style as charge, the command to read it would be:

topo readlammpsdata data.lammps charge

where data.lammps is the input LAMMPS data file given in the question. By changing the "Drawing Method" to CPK and "Coloring Method" to Index, you get the following: enter image description here
and you can see that there is no multiple bonds per atom here.

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1
  • $\begingroup$ Sorry, my question was incomplete. I run the configuration file in a lammps program, which I now included. The file I load into VMD is a .lammpstrj file. I still havent figured it out. Now it seems that just some random atoms are bounded. $\endgroup$
    – Jakob Boonen
    Commented Dec 13, 2021 at 19:14

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