From: alberto (voodoo.bender_at_gmail.com)
Date: Fri Mar 08 2019 - 04:14:34 CST

Hi,
I caluculated center of mass using lammps

# compute center of mass
compute comthf all chunk/atom molecule
compute mycomthf all com/chunk comthf
fix comthf all ave/time 200 1 200 c_mycomthf[*] file tmp.out mode vector

how can I visualize the results with vmd and calculate RDF with plugin in
vmd

my output is so for every step

1 17.6039 12.1194 4.01997
2 14.0353 11.0056 17.5689
3 7.45578 17.4733 17.8883
4 18.1058 6.45708 4.0776
5 9.76303 13.3352 5.99416
6 13.2716 2.8918 10.9596
7 17.3046 14.7731 10.7011
8 2.6502 12.5858 11.9348
9 14.8258 7.92377 7.48029
10 6.15659 14.5726 8.27535
11 9.28319 18.7508 8.5216
12 14.4473 17.7606 4.47159
13 6.65897 8.2071 5.89505
14 13.3466 12.3018 7.93919
15 1.79434 2.12821 2.37414
16 1.86264 9.36028 2.23349
17 18.6163 16.8443 6.8883
18 8.05732 2.83421 12.9543
19 18.4463 3.04727 14.2197
20 10.1412 12.0993 11.6887
21 16.6237 9.67259 12.7816
22 17.6829 18.3963 15.2288
23 5.65441 6.33326 16.3541
24 10.4968 2.18366 17.8385
25 3.00009 17.9523 4.50449
26 8.53922 18.0413 3.66535
27 1.45357 7.24204 13.6808
28 17.7654 1.76561 6.96114
29 2.44789 17.3328 11.1322
30 12.5438 2.83452 5.93666
31 4.35129 7.80461 9.55998
32 14.2653 2.83555 16.4165
33 14.1735 9.06885 1.79774
34 2.03591 18.0377 17.3614
35 11.9098 13.9987 1.50542
36 9.29191 9.95827 17.6383
37 17.2486 7.4673 18.1534
38 13.499 14.1254 14.5005
39 8.64627 2.52269 3.19608
40 15.0558 3.08233 1.41475
41 6.27941 16.3643 13.3715
42 3.02825 2.93906 11.546
43 5.62062 11.1696 14.6199
44 18.1995 5.7505 10.1769
45 5.9167 6.02849 1.75655
46 3.3566 2.84019 18.0663
47 13.7571 17.6894 8.9686
48 10.7145 7.51997 9.39653
49 9.7005 8.90452 2.37704
50 18.1586 17.4241 1.45047
51 6.09556 13.7684 1.98635
52 2.45972 12.1397 5.90685
53 11.6606 7.22456 14.1102
54 7.75756 2.72337 8.40756
55 18.6559 14.1111 17.0062
56 2.51979 3.43462 6.99281
57 13.6976 17.1107 18.1556
58 3.30391 13.3748 17.2509
59 11.4666 18.5815 13.9207

regards

Alberto