Dear Users. I'm trying to calculate the center of mass distance between cyclodextrine ( HAGD) and a biological molecule (MTX). I've searched on gromacs documentation in gmx distance
I use command line: gmx distance -f fixv1out.xtc -s bcd_mtx_solv_min.tpr -n fix.ndx -oav cmtransv1.xvg -select 'com of group "HAGD" plus com of group "MTX". On the index file (index.ndx) the names are correct (transcribed at the end of e-mail) However, I get the message bellow: Invalid index group reference(s) Cannot match 'group "HAGD"', because no such index group can be found. Cannot match 'group "MTX"', because no such index group can be found. Then, I used the index numbers for HAGD and MTX respectively. By doing so, I got the graphic but with wrong and unexpected results. I look the trajectory in VMD. What could I be doing wrong? What is the exact command for calculation of center of mass distance calculation between two groups A & B have in my index? Doing by the dist pair I manage to get a good result, but since cyclodextrine is cone shaped, I don't think that using the center of mass would be the best option. Index.ndx: [ HAGD ] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 [ MTX ] 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
