[gmx-users] Re: trjconv with multiple chains

devicerandom devicerandom at gmail.com
Mon Jan 10 18:32:07 CET 2011

On 10/01/11 08:43, yuanyuan wang wrote:
> sorry to say I can not found a center for the trj. I tried to make
> bigger box by trjconv -box -boxcenter, but it seems that the trj only
> exist in the old box area ,bigger box cannot stop jumps.
> Is it really happened that I can do nothing with it ?
> yuanyuan wang

Think about your problem a bit. What you see as jumps is just the 
molecule going from a side to another of your periodic box. In truth, 
the box has no sides. It's a continuous thing with a toroidal topology.

So, if your stuff diffuses freely in the box, you can never, ever avoid 
it walking through the "sides", because there are no sides: from the 
point of view of the molecule, it's all a continuous thing.

The only chance to visualize a mostly jump-less trajectory is that your 
stuff clumps together by aggregating into something definitely smaller 
than the box -and then you can center on the aggregate.

Hope it's clearer now,

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