[gmx-users] improper OPLS dihedrals in gromacs
Mark.Abraham at anu.edu.au
Wed Oct 19 16:37:29 CEST 2011
On 20/10/2011 12:26 AM, mu xiaojia wrote:
> 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
The quote below clearly says they are implemented as proper periodic
> 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?
These defined macros are used in the .rtp file, as your quote says. See
The types of numbers and their order match that for dihedral type 1 or
4, which are periodic. If they matched some other order then another
dihedral type would be implied - though this is admittedly a bit
perverse. See table 5.5. in the manual.
> 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?
The quote you make below confirms this.
> 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
> ; 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.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users