Dear Stefano
Leap is expecting the van der Waals radius of self-intraction (also known as "r_min") instead of sigma... to be more precise the half of it: R(ii)/2
You can check the relationship between "r_min" and sigma at Wikipedia [
https://es.wikipedia.org/wiki/Potencial_de_Lennard-Jones]
So the proper value you should use for a sigma of 2.20A is R(ii)= sigma*2^(1/6) = (2.20)*(1.12) ~ 2.469, then R(ii)/2 ~ 1.234
NONBON
Ti 1.234 0.580
Note, probably that many significant figures are not required...
Best,
MatÃas
----- Mensaje original -----
De: "Stefano Motta" <stefano.motta.unimib.it>
Para: amber.ambermd.org
Enviados: Jueves, 23 de Mayo 2019 11:31:17
Asunto: [AMBER] Lennard Jones parameters in frcmod
Dear Guys,
I'm trying to use some Lennard Jones parameters for unbound Ti but I'm
having some issues. The parameters are sigma=2.20 Angstrom epsilon=0.580
kcal/mol.
I added the following line to the frcmod file:
NONBON
Ti 2.2000 0.580
In the prmtop file the corresponding A coefficient is 3.0539*10^7, while
according to A=4*epsilon*sigma^12 I expected it to be 2.982*10^4.
Even during my simulation it seems that the VdW radii of this metal is too
large.
How can I correctly specify the LJ parameters?
Thanks
Best Regards
Stefano Motta
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Received on Thu May 23 2019 - 08:30:04 PDT
