[gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?

[Mark Abraham]

On 24/11/2010 5:04 AM, ms wrote:
> On 23/11/10 17:00, Mark Abraham wrote:
>> There is no general solution for bonds visualized on a
>> single set of coordinates, however - over a trajectory, either molecules
>> appear to diffuse out of the box, or appear to break.
>
> Yep, but if they appear broken because they are at the pbc boundaries 
> is no big deal. The problem (and with this I answer also Florian 
> Dommert) is that using -pbc tends to "break" stuff *inside* the box.

That can't be true in general. Use of one of the five different -pbc 
options, possibly with -center and -ur, possibly over several 
invocations has always worked for anything I've wanted. However it's 
hard to answer an assertion that something is broken if you don't know 
what the person has tried :-)

Mark