[gmx-users] COM
laura O.
laura.o.vendrame at gmail.com
Wed Jan 23 12:17:53 CET 2019
Hi
I used index.ndx too...but did not work.
Thanks
Em qua, 23 de jan de 2019 09:07, Quyen VuVan <vuqv.phys at gmail.com escreveu:
> He means, in your first email, your command is using fix.ndx and HAGD group
> is in your index.ndx, have you checked it?
>
> On Tue, Jan 22, 2019 at 7:54 PM laura O. <laura.o.vendrame at gmail.com>
> wrote:
>
> > Hi,
> >
> > I already used index.ndx at the line of code but the error kept the
> same. I
> > believe this is not the problem
> >
> > Thanks
> > Laura
> >
> > Em ter, 22 de jan de 2019 às 16:25, Joaquim Rui de Castro Rodrigues <
> > joaquim.rodrigues at ipleiria.pt> escreveu:
> >
> > > Hi,
> > >
> > > Your command line specifies -n fix.ndx but you seem to be editing a
> file
> > > named "index.ndx".
> > >
> > > HTH,
> > > Rui Rodrigues
> > >
> > > ________________________________________
> > > De: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> em nome de laura
> O. <
> > > laura.o.vendrame at gmail.com>
> > > Enviado: 22 de janeiro de 2019 17:31
> > > Para: gromacs.org_gmx-users at maillist.sys.kth.se
> > > Assunto: [gmx-users] COM
> > >
> > > 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
> > > --
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