unanswered Martini bead size vs equilibrium bond lengths for amino acids residues

  • subha
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2 years 1 month ago - 2 years 1 month ago #9379 by subha
I had a doubt regarding allowed bond lengths.
I was going through aminoacid.ff. I saw that it has two beads BB and SCI each of S and T bead type respectively. Now ST bead has a sigma value of 0.365nm (this is because of combination rule where the sigma value of cross interaction is (SIGMAii + SIGMAjj) /2 - softness_value. )
But the equilibrium bond length given is 0.27nm. Is that possible to have a bond length less than the allowed cross interaction sigma value? Or am I getting something wrong here.

I was wondering if the change of value has got to do something with the softness value of 0.01nm defined for martini3 beads except water.
Last edit: 2 years 1 month ago by subha.

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