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On Jul 31, 2022, at 3:41 PM, Roja <rose....@gmail.com> wrote:
Thank you so much for your help. Is this the same for calculating cos theta? or the water dipole vector instead of -OH vector?
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Am 8/1/22 um 07:02 schrieb Roja <rose....@gmail.com>:
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On Sep 20, 2022, at 7:02 AM, Roja <rose....@gmail.com> wrote:Hi,I am trying to calculate the distribution of angles between surface atoms of ZnS nanoparticle (type ZnB or type ZnC or type SB or type SC) and OH vector of water. But when I change the hw1 to hw2 in BA(hw1.positions - ow.positions or hw2.positions - ow.positions) I get different answers. Is there any way to specify that the code takes the hw vector closer to the surface (type ZnB or type ZnC or type SB or type SC)?
Best,Rose------------------npa = u.select_atoms("resname ZnS")water = u.select_atoms("same residue as name HW1 and around 2.38 (type ZnB or type ZnC or type SB or type SC)", periodic = True, updating=True) #Is it also possible to write: water = u.select_atoms("resname SOL and sphzone 6.0 (npa_com)") ?
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On Sep 22, 2022, at 5:49 AM, Roja <rose....@gmail.com> wrote:
Hi,
Thank you for your answer. I have tested this code and got an error for this part (resname SOL and sphzone {npa_com[0]} {npa_com[1]} {npa_com[2]}). So I changed it to (same residue as name SOL and point {npa_com[0]} {npa_com[1]} {npa_com[2]} 32.7). I guess the result is reasonable.
But now the problem is that when I want to calculate dipole vector of water (and these waters are the ones whose OH orientations have already been calculated by the code you sent me in the previous message). So the question is how should I select water molecules so that it takes the SOL molecules which the orientaion of their OH vectors has already been calculated? As you know the waters on the border (32.7 Å) are the problem right now. Hope I have explained it well:)
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