AMBER Archive (2008)

Subject: Re: AMBER: LJ parameters

From: aneesh cna (aneeshcna_at_gmail.com)
Date: Thu Apr 03 2008 - 06:30:39 CDT

hi Thomas,
               Thanks for your reply

On Wed, Apr 2, 2008 at 11:01 PM, Thomas Steinbrecher <steinbrt_at_scripps.edu>
wrote:

> Hi Aneesh,
>
> If you are confused about the actual values for the LJ parameters written
> into the topology file, they are computed like this:
>
> in sander, the LJ equation is A/r^12 - B/r^6. In parm.dat, the parameters
> correspond to this equation:
>
> 4 \eps [ 1/4 ( r0/r )^12 - 1/2 ( r0/r )^6 ]
>
> where r0 is the energy minimum in a vdw pair. Another commonly seen form
> of the LJ equation is:
>
> 4 \eps [ 1 / ( r/sigma )^12 - 1 / ( r/sigma )^6 ]
>
> with sigma giving the zero crossing of the curve ( r0 = 2^(1/6) sigma ).
>
> Every atom type contributes a given part to r0 which is given in the
> forcefield.
>
> An example where A and B come from for Cl:
>
> in parm99.dat:
> Cl 1.948 0.265
>
> Therefore for two Cl r0 = 3.896 A (2 x 1.948), epsilon = 0.265 kcal/mol
>
> in the prmtop, A and B are given then as:
>
> ACOEFF 3.24E06 = epsilon * r0^12
> BCOEFF 1.85E03 = 2 * epsilon * r0^6
>
> The reason these parameters are given that way is it eases computation,
> because A and B only need to be divided by the atom distance to get E(vdw).
> The same obfuscation is done with the atomic partial charges. This
> optimization is the reason why prmtop files are only semi-humanreadable...
>
> The reason for the zeros in the LJ fields is that many hydrogen atoms do
> not have a LJ potential centered on them, therefore they contribute only
> zeroes.
>
> Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> San Diego CA 92037, USA
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