[gmx-users] Protein jumping out of box

[Nuno R. L. Ferreira]

Hi Anna

That's not a problem ;) . Do not forget that you are working under peridic
boundary conditions, i.e. as if your system would be infinite. So, if a
molecule starts to diffuse, eventually the molecule will go outside your box
when it reaches the edge, cause its a finite box.  But since its a PBC
system, it will enter again into the box, in the same edge, or at the
opposite one.  And, because gmx holds a molecule as a "block", it doesn´t
break it.
Check the mailing list, because the question was adressed several times.

Regards,
Nuno

######################################
Nuno Ricardo Santos Loureiro da Silva Ferreira
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra - Portugal
Fax: +351 239 827703  - www.biolchem.qui.uc.pt
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----- Original Message ----- 
From: <herbst at fhi-berlin.mpg.de>
To: <gmx-users at gromacs.org>
Sent: Wednesday, July 28, 2004 11:59 AM
Subject: [gmx-users] Protein jumping out of box


Hello all,

I just run a 1 ns simulation for a protein in water and when I looked at
the trajectory, I saw that from one timestep to the next the protein
jumped out of the solvent (and the box), only to jump back in three
timesteps later. How can this happen and what can I do against it?

Thanks,
Anna
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