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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Received on Fri Apr 18 2008 - 21:16:13 PDT
