[gmx-users] COM

[laura O.]

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