The parameter data file is described here:
http://ambermd.org/formats.html#parm.dat although the upcoming AmberTools
user's manual will have an updated (and more comprehensive) version
courtesy of Romain Wolf.
On Fri, Jan 11, 2013 at 2:59 PM, Kirill Nuzhdin <knuzhdin.nd.edu> wrote:
> Dear All,
>
> I want to introduce simple radical into the water (explicit solvent,
> periodic system). Is the following statement correct: the radical is
> interacting with water molecules by coulomb + 12-6 potentials, two
> parameters for each of which could be given in frcmod.* file under
> NONBON section - A(for r^-12) and B(for r^-6) ?
>
Look under - 10B - in the website I gave you. The two numbers are Rmin
(the van der Waals radius) and epsilon (the well depth of the 6-12
potential). These are combined, inside tleap, into the A and B
coefficients. Details are provided in
http://ambermd.org/vdwequation.pdf.
Rmin is in Angstroms, epsilon is in kcal/mol.
1. what are the units for these parameters?
> 2. are there any description for the format of this file? (what is the
> second number in MASS section?)
>
The second number of the MASS section is the atomic polarizability. It's
not used for anything to my knowledge.
> 3. how to set different potentials for interaction with different atoms?
> I.e. Hx...OW - one potential, and Hx...HW - another.
> 4. is it possible to set a different potential form, other then 12-6 ?
>
The 10-12 potential form is 'supported', but uncommon. Other than these
two options, you'll need to write your own code for it.
> If I want to calculate the radical using external QM program, what
> information about non-QM environment would be sent to the program? Point
> charges?
>
Yes.
> Is it possible to use LES with QM?
>
Probably not, but I am not sure.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jan 11 2013 - 13:30:02 PST
