[gmx-users] whole/center/inbox

[Yiannis]

Give a try to
trjconv -center -pbc com

Ioannis

Le jeudi, 1 jul 2004, à 18:20 Europe/Paris, Bruno Pagano a écrit :

> I am trying to get a continuous trajectory centered in the box with a 
> whole
> molecule...
> shouldn't be that difficult....
> but whatever I try I do not manage.
>
> I have a whole starting structure, I can get first a whole trajectory, 
> then I
> run nojump, then I would like to center that but all the atoms diffuse 
> out of
> the box...
> how I can get then finally a trajectory without diffusion?
> If I then run trjconv  -center to center the previously obtained 
> trajectory
> (from whole and then nojump) visualising with vmd I have a no conection
> between the atoms anymore....
>
> Thanks
>
> Bruno
> -- 
> Dr. Bruno Pagano
> Mathematical Biology Division
> National Institute for Medical Research
> The Ridgeway, Mill Hill
> NW7 1AA London
> tel (direct) 02088162396
> fax 0208 906 4477 /02088162460
> http://mathbio.nimr.mrc.ac.uk
>
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