[gmx-users] COM

[laura O.]

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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