[gmx-users] .mdp settings for CHARMM36

Gregory Poon gpoon at gsu.edu
Thu Apr 28 23:22:04 CEST 2016

Hello everyone,

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 
following note:

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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