[gmx-users] charmm27 in gromacs

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 15 04:41:58 CET 2012

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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