[gmx-users] rm_pbc

[Christoph Freudenberger]

Anton Feenstra wrote:
> rm_pbc makes molecules whole again. 
Sorry if this wasn't clear from the first message.
The main question is: Would the outcome for pbc_dx
be affected from wether a topology has been read or not?
As far as I understan it right now, the top is only needed
to make the molecules whole again.

> mdrun only writes whole
> molecules, but one might want to analyze output from other
> programs. In order for rm_pbc to know which atoms are bound
> together in one molecule, it needs the topology.
> In most analysis tools, the topology is now actually optional,
> in which case the user should know if her molecules are whole.
So I should also put that option back in...

> By the way, 'cleaning' g_rdf was a good idea. I've done some
> of the rough 'demolition'-type of cleaning some time ago, but
> didn't have time nor incentive to do the tiny things.

Well... there's not so much left from the original code now :-)

regards
-- 
Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785