[gmx-users] Polymer in periodic boundary conditions again

[K.A. Feenstra]

Ester Chiessi wrote:
> Hi all,
> 
>
> My work for building a polymer in periodic boundary conditions is going on.
> Thanks a lot!

You're welcome.

[...]
> My idea is to 'correct' the coordinates of the polymer by translation of the right
> amount and to repeat the minimization.
> 
> Are there any suggestion?

You might try the following (which is what I intended to say in the
first place):
1) energy minimze your non-inifinte polymer.
2) Probably the end points will no longer be 'periodically aligned'
    at the box edges; correct that by rotation and/or adjusting the
    size of the box (I expect your molecule to shrink a little).
    You might have to remove some water (or, throw away your water and
    use genbox again).
3) switch to the 'explicitly connected' (i.e. infinite) topology and
    energy minimize again.
The reason for this is that if you only minimize the infinite molecule,
you will always have the total length kept fixed, since it must be the
same as you box length. This way you can first let the molecule adjust
its length, and then in the next step let the molecule adjust to the
infinite periodicity.


-- 
Groetjes,

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