Input files
The following are files read by amk, and therefore, they must be present in wrkdir.
name.xyz
Where name refers to the name for our system (FA.xyz in our example). The recommendation is to use acronyms like FA for Formic Acid or short names. This file contains an initial input structure of our system in XYZ format:
5
C 0.000000 0.000000 0.000000
O 0.000000 0.000000 1.220000
O 1.212436 0.000000 -0.700000
H -0.943102 0.000000 -0.544500
H 1.038843 0.000000 -1.634005
Please provide here a stable conformer of the reactant molecule. A general recommendation is to use a structure previously optimized with the method selected with the keyword LowLevel or eventually LowLevel_TSopt. If your input structure is fragmented, then, kinetics results, if available, are meaningless. In this case you should use biased MD to smash together the fragments and obtain a TS for the bimolecular process, like in the diels_alder example.
This file is mandatory except for association and vdW samplings where two XYZ files are needed instead.
Avoid using integers for any of the XYZ coordinates, as this will cause problems with the high-level calculations.
name.dat
Where name can be any name, from just the name of the system to something that identifies the type of calculation you are carrying out; in our case FA.dat. This file contains all parameters of the calculation and has different sections, which are explained as follows. This file is mandatory in all cases.
Example of the FA.dat file:
--General--
molecule FA
LowLevel mopac pm7
HighLevel g09 hf/sto-3g
HL_rxn_network complete
IRCpoints 29
charge 0
mult 1
--Method--
sampling MD
ntraj 10
barrierless yes
--Screening--
imagmin 200
MAPEmax 0.008
BAPEmax 2.5
eigLmax 0.1
--Kinetics--
Energy 150
The file name.dat is organized in four sections: General, Method, Screening and Kinetics, which are explained in detail below. Each section contains lines with several keyword value(s) pairs with the following syntax:
keyword value(s)
keyword is a case-sensitive string and it must be the first field of the line.
value(s) can be strings, integers or floats and is/are the value(s) of the keyword.
At least one blank space must be kept between keyword and value(s). A few keywords include some additional lines right below the keyword line (see Biased dynamics).
Next, you will find a detailed explanation of the keywords grouped together in the different sections. For each section, only the most important keywords are described. Additional keywords can be found in Other capabilities.