[gmx-users] COM

[laura O.]

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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