Re: [AMBER] Lennard Jones parameters in frcmod

From: Matias Machado <>
Date: Thu, 23 May 2019 12:21:56 -0300 (UYT)

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 []

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

  Ti 1.234 0.580

Note, probably that many significant figures are not required...



----- Mensaje original -----
De: "Stefano Motta" <>
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
I added the following line to the frcmod file:

  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
How can I correctly specify the LJ parameters?

Best Regards

Stefano Motta
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Received on Thu May 23 2019 - 08:30:04 PDT
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