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Combining boxes of different solutes

Returning to xleap again.
The box I require this time has little tricky requirements.
1) The box should satisfy the molarity ratio for the solute: solvent.
2) Should be big enough that QMMM calculations can be carried out easily
3) combine sets of molecule-pairs which are interconvertible following a proton transfer.

I have a pair of molecules say p(H)--i which can be converted to another set called P--I(H) following a proton transfer from p to i.So,

p(H)--i <---> P-I(H)

To fulfill condition (1), I initially created one molar box for p(H)--i called "PIN" and other box for P--I(H) called "PII"

For condition (2) and (3), I created a bigger box with 7 PIN and 1 PII boxes.

The idea is: after proton transfer from I to P, during the QMMM calculation, P--I(H) pair coming from "PII" should convert to p(H)--i pair like other pairs from "PIN" and the whole box should become homogeneous with 8 p(H)--i pairs.


We begin with:
PIN with box size of [17.749 16.372 17.147] and
PII with box size of [17.141 16.064 18.603]

Load PIN and PII boxes

>loadoff PIN.lib
> loadoff PII.lib

Check dimensions of the box.

> setbox PIN centers
  removing previous box..
Box dimensions:  17.749000 16.372000 17.147000
> setbox PII centers
 removing previous box..
Box dimensions:  17.141000 16.064000 18.603000

step 1: translate PIN in X-direction

> ONE=copy PIN
> translate ONE{17.749 0.0 0.0}
> TWO=combine{PIN ONE}
> edit TWO

step 2: translate TWO in Y-direction

> THRA=copy TWO
> translate THRA{0.0 16.372 0.0}
> THR=combine{TWO THRA}
> edit THR



So, now we have generated a bigger box "FOUR" containing four "PIN" boxes. It has 4 pairs of p(H)--i.

We need to add 3 more PIN boxes to the system to make a total of 7 pairs of p(H)--i.

step 3: translate TWO in Z-direction

> FOURA=copy TWO
> translate FOURA {0.0 0.0 17.147}
> FOUR =combine{THR FOURA}
> edit FOUR


We need to add one more PIN box to the system

step 4: translate PIN in the Z-direction

> FIVA=copy PIN
> translate FIVA {0.0 16.372 17.147}
> SIX=combine{FOUR FIVA}
> edit FIV

Now the final task to add one box of PII to this system containing 7 boxes of PIN

step 5: translate PII in X-, Y-, Z- direction

> SEVA=copy PII
> translate SEVA {17.749 16.372 17.147}
> SEV=combine {FIV SEVA}
> edit SEV



Structure SEV is a bigger box containing 7 one molar boxes of PIN and one box of one molar PII.

> Box dimensions:  35.498000 32.744000 34.541230

This bigger box can be used as an initial point. We must equilibrate this box first in NVT, NPT conditions before we run a production NVT to use it for further simulations.
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