[gmx-users] COM

[laura O.]

Hi,
Thanks
but I already tried without the double quotation marks but the result was
the same.

---------------------------------------------------------------------------------------------------------------------------------
  Cannot match 'group "HAGD"', because no such index group can be found.
  Cannot match 'group "MTX"', because no such index group can be found.


Em ter, 22 de jan de 2019 às 16:01, Quyen VuVan <vuqv.phys at gmail.com>
escreveu:

> Hi,
> I don't think you need a double quote in your select HAGD
>
> On Tue, Jan 22, 2019 at 6:32 PM laura O. <laura.o.vendrame at gmail.com>
> wrote:
>
> > 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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