[gmx-users] help with improper angle in gmx

[Justin Lemkul]

On 1/7/13 6:11 PM, Tom wrote:
> Dear Gromacs Users
>
> I want to use harmonic type of improper angle potential with opls-aa
>
> The manu seems not clear.
>
> Can anyone give an small example about the format in *rtp file
> and ffbond.itp file?
>

The names of improper_*_*_*_* tell you to what improper the parameters apply. 
X, Y, and Z are used to indicate any atom.  The only other atoms used are the 
types that can be used in those positions, i.e. O_C_X_Y is the improper about a 
carbonyl, while Z_N_X_Y is used in amide groups (peptide bonds).

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================