questions on dihederal and 1-3 repulsion potential

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1

  1. To assign 1-3 repulsion term (atoms separated by two bonds) of force field, what command should I use?

  2. I’d like to include independent dihedral terms for cis (i-j-k-l) and trans (i-j-k-l’) cases where k is connected to j, l, and l’ (i-j-k-l and i-j-k-l’ are almost planar and the equil. dihedral angle is 0 for i-j-k-l while it is 180 for i-j-k-l’).
    How can I define i,j,k,l,l’ for it?
    Is it enough for it by employing two commands line assigning different dihedral types (e.g., 1,2) and using phi of 0, 180 respectively?

Thanks for your help in advance.
Best regards,

Luke

2

2011/7/26 JhonY. I. <yijhon@…8…>

  1. To assign 1-3 repulsion term (atoms separated by two bonds) of force field, what command should I use?

How are the atoms repelled? Is it via standard force field form? If so, then you can use the special_bonds command to tell LAMMPS to allow for something different than the default. If it’s not something that LAMMPS has built-in, you’ll need to modify the code to do it.

  1. I’d like to include independent dihedral terms for cis (i-j-k-l) and trans (i-j-k-l’) cases where k is connected to j, l, and l’ (i-j-k-l and i-j-k-l’ are almost planar and the equil. dihedral angle is 0 for i-j-k-l while it is 180 for i-j-k-l’).
    How can I define i,j,k,l,l’ for it?
    Is it enough for it by employing two commands line assigning different dihedral types (e.g., 1,2) and using phi of 0, 180 respectively?

Yes, you should be able to do it by defining two different types with different values for the corresponding coefficients in the potential.

–AEI