these videos are great! thank you for such amazing content! looking forward to future videos? so, i watched your torsion video and i was wondering from this video.. is the whole point of using the out-of-plane angles for the purposes of replacing torsion where torsion can't be calculated? so for the formaldehyde example, are you not able to find the torsion of H-C-H-O? thanks in advance for any help!
Hi Bryant. Yes, anything that can be accomplished with out-of-planes can be done with torsions as well. In the torsion video I define a torsion to be a quartet of atoms (1-2-3-4) where 1-2, 2-3, and 3-4 are bonds. For out-of-planes, 1-3, 2-3, and 3-4 are bonds (all exterior atoms are bonded to the same central atom). In the case of formaldehyde, the carbonyl carbon is the central atom, and there technically is not a torsion to help maintain the planarity of the molecule. In some force fields they use "improper torsion" where they define a torsion in which one of the three atom pairs isn't bonded, but it helps to maintain a planar sp2 center. The math is slightly different, but in practice nearly identical results can be achieved. Some people use out-of-plane angles and improper torsion angles as interchangeable synonyms.
thank you! i think that makes sense, i have been working on the 2nd case you mentioned where one of the three atom pairs isn't bonded (i think you call it improper torsion?) where the torsion is dependent on xyz positions and not necessarily the bonds. if the math is indeed different, you have answered my question! i've been trying to use a torsion equation on an out-of-plane-like arrangement of atoms but each time, i end up getting a compilation error for having a negative square root when calculating the sine of an angle. since you say that the math is different, i think my next best option is to use a logic statement to avoid this torsion calculation so that i can apply an out-of-plane calculation. hopefully this is the right direction, thanks again!
Just Excellent content!
pls help me how to add frame.file into this molecule, now I just have 1 frame for this molecule, so I cannot make my molecule vibrated
these videos are great! thank you for such amazing content! looking forward to future videos?
so, i watched your torsion video and i was wondering from this video.. is the whole point of using the out-of-plane angles for the purposes of replacing torsion where torsion can't be calculated? so for the formaldehyde example, are you not able to find the torsion of H-C-H-O? thanks in advance for any help!
Hi Bryant. Yes, anything that can be accomplished with out-of-planes can be done with torsions as well. In the torsion video I define a torsion to be a quartet of atoms (1-2-3-4) where 1-2, 2-3, and 3-4 are bonds. For out-of-planes, 1-3, 2-3, and 3-4 are bonds (all exterior atoms are bonded to the same central atom). In the case of formaldehyde, the carbonyl carbon is the central atom, and there technically is not a torsion to help maintain the planarity of the molecule. In some force fields they use "improper torsion" where they define a torsion in which one of the three atom pairs isn't bonded, but it helps to maintain a planar sp2 center. The math is slightly different, but in practice nearly identical results can be achieved. Some people use out-of-plane angles and improper torsion angles as interchangeable synonyms.
thank you! i think that makes sense, i have been working on the 2nd case you mentioned where one of the three atom pairs isn't bonded (i think you call it improper torsion?) where the torsion is dependent on xyz positions and not necessarily the bonds. if the math is indeed different, you have answered my question! i've been trying to use a torsion equation on an out-of-plane-like arrangement of atoms but each time, i end up getting a compilation error for having a negative square root when calculating the sine of an angle. since you say that the math is different, i think my next best option is to use a logic statement to avoid this torsion calculation so that i can apply an out-of-plane calculation. hopefully this is the right direction, thanks again!
thank u so much
these videos are extremely educational
trying to code all the stuff in C++
wouldn't normal vector n_jlk dot r_li equal r_li * cos(phi) rather than cos(phi)?
i saw formaldihide
The example molecule is indeed formaldehyde.