[gmx-users] COM

[Quyen VuVan]

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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