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
--
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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
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