Re: [AMBER] matching paramters of methane

From: David A Case <>
Date: Thu, 16 Jul 2020 12:36:28 -0400

On Thu, Jul 16, 2020, angad sharma wrote:

>I generated a topology file of methane. And in that file the values of
>ACOEFF and BCOEFF are as follows:

> 1.04308023E+06 9.71708117E+04 7.51607703E+03

> 6.75612247E+02 1.26919150E+02 2.17257828E+01

Check the order here: the first value is for C-C interactions; I
think(?) the second is for C-H interactions, and the third for H-H
interactions. Parmed can help here.

>Actually i want to know how these values came so, with parmed i got values
>of LJ parameters which are as:
>and I think the units of lj radius(radius) are *kcal/mol* and of
>epsilon(depth) is in *angstrom.*

It's the reverse: radius in Ang, well-depth in kcal/mol.

>manually Aij 1018.6330 94.7933

How did you do the "manual" calculation? Remember that the Rmin value
for a C-C interaction is twice the radius Parmed reports for a single
C atom.

>units Aij manually (kcal/mol angstrom^12)
>units Bij manually (kcal/mol angstrom^6)

These are the correct units.


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Received on Thu Jul 16 2020 - 10:00:03 PDT
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