[gmx-users] improper OPLS dihedrals in gromacs

[Richard Broadbent]

Dear Jia,


>I found a question in 2009 asking which format of improper does
>OPLS dihedral gromacs use. I have the same question, is it periodic or
>harmonic? If it is periodic, why in its ffbonded.itp file: #define
>improper_O_C_X_Y 180.0 43.93200 2 what do they mean?

this means that the dihedral will be calculated as:
43.93200*(1+cos(2*x+180.0)) = 43.93200*(1-cos(2*x))

>Also, when I plug in tinker's improper dihedrals(which should be
>harmonic) into gromacs, the results matches well whith each >
>other(tinker and gromacs). Does it suggest that gromacs uses a periodic
>dihedral?

I'm not sure I understand you're question as that's stated explicitly
below. However, the taylor expansion of the periodic improper is 

2*x^2-(2/3)*x^4 +O(x^6)

Therefore a harmonic approximation is quite good for the interaction. (|
x|<15 degrees the error is less that 2.5%)


I hope that clears things up.

Richard

-----Original Message-----
From: mu xiaojia <muxiaojia2010 at gmail.com>
Reply-to: Discussion list for GROMACS users <gmx-users at gromacs.org>
To: gmx-users at gromacs.org
Subject: [gmx-users] improper OPLS dihedrals in gromacs
Date: Wed, 19 Oct 2011 08:26:25 -0500

Dear GMX-users, 

I found a question in 2009 asking which format of improper does
OPLS dihedral gromacs use. I have the same question, is it periodic or
harmonic? If it is periodic, why in its ffbonded.itp file: #define
improper_O_C_X_Y 180.0 43.93200 2 what do they mean? Also, when I plug
in tinker's improper dihedrals(which should be harmonic) into gromacs,
the results matches well whith each other(tinker and gromacs). Does it
suggest that gromacs uses a periodic dihedral? 

Thanks, here is the part I quoted from ffbonded.itp 

[ dihedraltypes ] ; 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. 

--jia 
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