[gmx-users] Protein-DNA simulation LINKS error

[Timofey Tyugashev]

Just to make sure I want to recheck myself:
Lennard-Jones interactions cutoffs (set at 10A in the paper) are defined 
by rvdw
short-range electrostatic interactions (set at 10A in the paper two) are 
defined by rlist and rcoulomb, but when I use Verlet scheme, rlist is 
ignored anyway.
long-range electrostatic interactions (they are specified separately in 
AMBER99SB-ildn paper at 10,5A) are defined by rlistlong. Are there any 
other parameters I need to set to use this twin-range cutoff scheme?
24.06.2015 18:25, gromacs.org_gmx-users-request at maillist.sys.kth.se пишет:
> Read the AMBER99sb-ILDN paper.  Use those values.  You can't pick some arbitrary
> value in the ballpark of what different models use.  That doesn't make sense.
> Cutoffs are part of the force field; treat them as such.
>
> Your problem almost certainly comes from an inaccurate 8-oxoG topology if normal
> guanine works fine.
>
> -Justin