[gmx-users] Amorphous polymer and periodic box

[Erik Lindahl]

Hi,

>ant to have an infinite molecule. Is
>that correct? This can be done, but you have to set an environment
>variable to tell GROMACS that you want to do the full periodic bundary
>calculations (as opposed to our optimized scheme).
>setenv GMXFULLPBC 1
>
>If you do not have an infinite molecule it is usually fine, as long as
>your molecule is shorter than 3 box lengths, otherwise the same env.
>var. has to be set.
>
No, you don't need to set that for large molecules anymore; since 
version 3.0 the shift code handles
arbitrary molecular shifts.

The normal way to simulate polymers is to have a long molecule and let 
it interact with itself if it's
longer than the box. You'll probably have to start with an extended 
molecule in a very long box at
higher temperature, and then gradually use pressure scaling to shrink 
the box (and let the molecule
cross the box boundary).


I'm not sure how well the Gromacs/Gromos forcefields do for long 
homopolymers; there is a special
poylethylene forcefield by Boyd and coworkers - it's included in the 
poly-ch2 benchmark on our
webpage (so you can find the files to use in the benchmark tarball)

Cheers,

Erik