See, as there are 4 tubes, shown in 2 lines, see it as a matrix of 2x2.
As per your information, both the diameters are same.
X Y Z
Line 1: 15 7 27
Line 2: 15 7 27
(All are in Å units)
Water is 10Å thick, 20, 17, 10 in X,Y,Z.
I guess, do the following steps.
1. Set a box with dimensions, 15 7 27. This dimension wont allow any
interstitial space, to solve your first problem.
2. As water TIP3PBOX unit is considered 2.8Å in length, solvate till
the 10Å, which will add water molecules.
3. Now check the confirmation.
4. If it is correct, do step 5. Else relax the structure with some 500 cycles.
5. Apply another box of 20, 17,10 finally and apply periodic volume
from there onwards.
Do let me know, about it.
--
Ashish Runthala,
Faculty Division III,
Assistant Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031
INDIA
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Received on Wed Aug 19 2009 - 22:44:57 PDT
