On 11/11/2011 3:01 AM, James Starlight wrote:
Mark,
I've mistaken
I need to invert impropers for DIHEDRAL for Calpha atom. By this way I
want to change L form to D form for Gromos ff. Does this correct ?
[ dihedrals ]
; ai aj ak al gromos type
-CA -C N CA gd_14
-C N CA C gd_39
N CA CB CG gd_34
N CA C +N gd_40
CA CB CG CD1 gd_34
I've no idea what any of the above was intended to mean. I'll repeat
myself again, there's nothing about the improper dihedrals that enforces
a particular chirality. Proper dihedrals also don't care about
chirality. Chirality is set in the starting configuration, and merely
preserved by the force field.
So I think that I need to make corrections in that gd_n files. But in
what exactly and where in manual could I read about that parametrisation ?
See the #defines in ffbonded.itp. The implementation of the GROMOS force
fields are a bit idiosyncratic this way.
Mark
It could be cool that in that section such information present :)
http://www.gromacs.org/Documentation/Terminology/Dihedral?highlight=dihedral
2011/11/10 Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
First, identify that there's anything to invert. Look at the
#define lines for gi_1 and gi_2 and the manual sections for
impropers. There's nothing associated with any handedness. The
impropers for chirality prevent inversion, rather than enforcing a
particular chirality. You can test this yourself. Make a .tpr of
an L-amino acid and .gro files of each chirality, and then use
mdrun -rerun Lconfiguration.gro -s Lconfiguration and compare with
mdrun -rerun Rconfiguration.gro -s Lconfiguration.
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