[gmx-users] Polymer in periodic boundary conditions

[Erik Lindahl]

Ester Chiessi wrote:

>Hi gromacs users,
>
>I'm trying to build an infinite chain in periodic boundary conditions..
>
>I saw I have to use:
>
>setenv GMXFULLPBC.
>
No, you shouldn't use this anymore. It just slows things down and I 
changed the code already in 3.0
so that we can handle arbitrary molecules!

>
>The question is how to insert in the topology file the information that
>the last atom of the chain has to be covalently bound to the periodic
>image of the first .
>
>Should I have to use the same residue name for each repetitive unit (
>i.e. no end-residues) only giving the connectivity to the preceeding
>residue and then choose the exact box lenght to contain the part of the
>chain I'm defining in the topology?
>
Most people simulating long polymers (1000-10000 units) don't care about 
binding the last and first
units - they have a very long chain instead. This makes it much easier 
to equilibrate the system.

Just put a long polymer in a very large box and let the box collapse or 
shrink around it. I think this
is usually done at something like 600K. You might want to check the work 
of Boyd et al.

Cheers,

Erik