GROMACS version:
GROMACS modification: Yes/No
Hello,
I modified a DNA phosphate at O1P vs O2P, which chemically creates a chiral phosphate (Rp/Sp). However, in GROMACS I obtain identical trajectories for both cases.
According to the GROMACS documentation:
“A special type of dihedral interaction (called improper dihedral) is used to force atoms to remain in a plane or to prevent transition to a configuration of opposite chirality (a mirror image).”
Based on this, I expected different improper definitions for the two cases.
For both modifications, the [ impropers ] section is identical:
Modification on O1P
[ impropers ]
; IMPROPERS FROM DEOXYADENOSINE
C6 C5 N1 N6
N6 H61 H62 C6
Modification on O2P
[ impropers ]
; IMPROPERS FROM DEOXYADENOSINE
C6 C5 N1 N6
N6 H61 H62 C6
I would highly appreciate any guidance on whether additional chiral impropers or asymmetric parameters are required to distinguish Rp/Sp phosphates in GROMACS.