[gmx-users] .mdp settings for CHARMM36
gpoon at gsu.edu
Thu Apr 28 23:22:04 CEST 2016
I would like to know if the prescribed settings for CHARMM36
specifically regarding constraints = h-bonds, apply to all steps (em,
nvt, npt, etc). I am assuming so, but I am asking because setting
constraints = h-bonds gave an energy-minimized DNA structure the
NOTE 1 [file topol.top, line 50]:
The bond in molecule-type DNA_chain_A between atoms 490 C2 and 491 O2 has
an estimated oscillational period of 1.9e-02 ps, which is less than 10
times the time step of 2.0e-03 ps.
Maybe you forgot to change the constraints mdp option.
which is not present if constraints = all-bonds. Obviously my question
reflects my lack of understanding of what is really going on, so I
appreciate all the insight I can get.
Thanks in advance,
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