[gmx-users] .mdp settings for CHARMM36

Justin Lemkul jalemkul at vt.edu
Thu Apr 28 23:41:01 CEST 2016

On 4/28/16 5:21 PM, Gregory Poon wrote:
> Hello everyone,
> I would like to know if the prescribed settings for CHARMM36
> (http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM),
> 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.

constraints = h-bonds is correct.  See previous posts on this topic for 
extensive discussion on why this is the case.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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