[gmx-users] Center

[Nuno R. L. Ferreira]

Raghunadha Reddy Burri <burri at heineken.chemie.uni-dortmund.de> escreveu:

> Dear GMX users,
> 
> In my simulation of protein and water frequently going out of cubic box! 
> 
> Periodic boundary conditions in all directions means no more out of box 
> ( because every side have another box same as current box) but really I do 
> not understand how some of simulation frames showing protein (some time 
water 
> also) going out of box, this is really getting problem to make a movie 
from 
> trajectory file.
> 
> How can possible to maintain protein in cubic box?

Check trjconv command.
Search the mailing list also. Some similar questions were already discussed.

Regrads,
Nuno

P.S. PBC indeed means that the 3D space is replicated. How? If one water 
molecule goes out of the box in a certain edge, it will enter in the 
opposite edge. This is called the wrap process. But you can have a MD sim. 
without wraping, and what you see in this case, is (assuming a cubic box) a 
cube of molecules at time=0, and then you see all the molecules going in or 
out of that initial box. In this case, you are seeing a continuous 
trajectory.
But I think you are just seeing a protein jumping from one side to another, 
no problem with that.

> 
> Looking for positive reply.
> 
> Thank you for your time and consideration.
> 
> Till Then
> 
> Burri
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-- 
-----------------------------------------------------
Nuno Ricardo Santos Loureiro da Silva Ferreira
Ph.D student
Grupo de Química Biológica
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra
Portugal
www.biolchem.qui.uc.pt
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\" Do not worry about your dificulties in mathematics.
   I can assure you that mine are still greater.\"
                                       e=mc2
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