Tom wrote:
Dear Gmx Developer or Users,
Can anyone explain which section is for the parameters of improper
dihedral angle
on the file of ffbonded.itp ?
On the file of ffbonded.itp, there is not any comment to differentiate
the proper and improper
dihedral angle.
E.g. on thie file of ffbonded.itp in the directory of charmm27.ff
There are two sections about dihedral angle:
[ dihedraltypes ]
; i j k l func phi0 cp mult
C CT1 NH1 C * 9* 180.00 0.8368 1
......
[ dihedraltypes ]
; i j k l func q0 cq
CPB CPA NPH CPA * 2* 0.0000 174.0544
..........
There is also no explaination the explaination about the function type 2.
Table 5.5 of the manual lists all function types, what they are, and what the
required parameters are. Functional forms are discussed in section 4.2.
It seems difficult for users to edit the parameters.
Comprehensive explanations of all nuts and bolts are beyond what can be included
in the manual or force field files. A deep knowledge of the underlying force
field (which may span several published papers, other manuals, etc) is required
to understand any of the force fields implemented in Gromacs (or any other
software, for that matter).
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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