[gmx-users] Dihedrals Parametrization in the .rtpf File

[Justin A. Lemkul]

Lara Bunte wrote:
> Hi
> 
> I have three questions:
> 
> 
> 1.)
> 
> If you create a .rtp file in your force field folder (I use charmm27) you
> have a block [ dihedrals ] with the structure
> 
> [ dihedrals ]
> 
> 
> atom1    atom2    atom3    atom4    phi0    cp      mult
> 
> 
> What is cp and what is mult?
> 

Force constant (I believe) and multiplicity.

> 
> 2.)
> 
> In the [ impropers ] block you have
> 
> [ impropers ]
> 
> 
> atom1      atom2      atom3      atom4     q0     cq
> 
> What is q0 and cq?
> 

Equilibrium angle and force constant.

> 3.) Out of a supporting information of a paper I have the information
> "improper dihedral angles" I have the four atoms and force constants and
> equilibrium angles. What is the syntax for thin in my .rtp file? Do I use [
> dihedrals ] or [ impropers ] block or how do I write my Information in
> gromacs in my rtp. file?
> 
> 

In an .rtp file, you use [dihedrals] for dihedrals and [impropers] for improper 
dihedrals - in ffbonded.itp you would specify parameters for the impropers 
within a [dihedraltypes] block and specifying the correct function type for the 
interaction.

-Justin

-- 
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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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