[gmx-users] whole/center/inbox

[Bruno Pagano]

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