Hello,
I have two separate questions. If I should submit two seperate requests in
the future, please let me know. I am just trying to not spam peoples email
boxes!
1. I am implementing the amber force field (want to use GAFF parameters) in
a MD code my research group is developing. Its my understanding that the
bond and angle spring constants are not multiplied by 0.5. However, its my
understanding that the functional form of the dihedral/improper energy is
E = 0.5*k*(1+cos(n*phi - d) )
I have a prmtop file that looks like
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
1.55555556E-01 0.00000000E+00 1.10000000E+00
Could someone tell me if these spring constants have already been
multiplied by 0.5 or not?
2. I am wondering about whether there are issues I should be aware of
associated with truncation error when converting from the epsilon sigma
representation of the lennard jones interaction to the amber epsilon rmin
representation. For instance, in the case of the SPC/E water model, I
believe the sigma value is given as 3.166. Converting that to Rmin for
AMBER
rmin = 1.77685742 --> 1.777 if we carry the same precision through
Is it correct to make this kind of truncation if I am going to hand type
the parameters prior to a simulation, as I need to do in my groups code or
in lammps since i don't have access to moltemplate, or could even that
subtle of a change in the parameters lead to disastrous consequences?
--
B.S.E in Chemical Engineering, University of Michigan, 2012
PhD candidate in Chemical Engineering, Purdue University
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Received on Wed Oct 07 2015 - 22:00:03 PDT
