[gmx-users] Polymer in periodic boundary conditions

[K.A. Feenstra]

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.
> 
> 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 .

There is no distinction between an atom and any of its periodic images.
So, you simply define a bond between the appropriate atom in the last
residue and the atom in the first residue.

> 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?

Yes.

> Is it important to start with an orientation of the chain which
> geometrically satisfies the periodicity requirement?

Yes.
You can use editconf to orient your polymer along its principal axes.
That will probably already be very close to the periodically
consistent orientation.

> Is it possible to solvate the polymer and use the PBC jet?

Yes.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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