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

ms devicerandom at gmail.com
Wed Nov 24 15:35:23 CET 2010

On 24/11/10 02:47, Mark Abraham wrote:
> 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 :-)

You are absolutely right, but well, it was not needed for the aestethic 
purposes so far required :)

Of course if and when needed for analysis, I'll try harder with trjconv 
-pbc arcanes.


Massimo Sandal, Ph.D.

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