[gmx-users] Re: help with improper angle in gmx

Justin Lemkul jalemkul at vt.edu
Tue Jan 8 16:40:15 CET 2013

On 1/8/13 10:34 AM, Tom wrote:
> Thanks for your reply, Justin!
> I knew that gmx use as the follows for opls aa:
> --------------------
> ; Improper OPLS dihedrals to keep groups planar.
> ; (OPLS doesnt use impropers for chiral atoms).
> ; Since these functions are periodic of the form 1-cos(2*x), they are actually
> ; implemented as proper dihedrals [1+cos(2*x+180)] for the moment,
> ; to keep things compatible.
> ; The defines are used in ffoplsaa.rtp or directly in your .top file.
> ; O?-C -X -Y improper torsion. C can be C_2 or C_3 too.
> #define improper_O_C_X_Y        180.0     43.93200   2
> --------------------
> But if it is possible to choose the function type: harmonic type  (f.t y. =2)
> Where to assign function type number? Thanks!

The function type is a built-in part of the force field.  Consult table 5.5 in 
the manual for the different function types and what they require.  A function 
type is set in the .top file when specifying a given interaction, but you can't 
simply choose to use a harmonic improper dihedral when the force field 
prescribes a periodic improper dihedral, as in the case of OPLS.  You'll get 
fatal errors about syntax and such, which should tell you that you're messing 
with the force field in an unacceptable way.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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