[gmx-users] question about OPLS-AA force field -required bond constraints
jalemkul at vt.edu
Thu Oct 10 18:27:18 CEST 2013
On 10/10/13 12:17 PM, Martin, Erik W wrote:
> Hi, I'm new to both Gromacs and OPLS. I have always used CHARMM or AMBER
> before so am a bit confused about some idiosyncrasies.
> When I go to a production run on my system (a protein in a truncated
> octahedron box of Tip4 water) I have removed all constraints. When I run
> grompp, I get an error telling me that a bond between a HG proton and OG
> oxygen of protein has an oscillation period of 9e-3 ps and is incompatible
> with my 1 fs time step. I am used to being able to run a completely
> unconstrained simulation with a 1 fs time step… so I'm assuming this is a
> property of OPLS-AA?
No, it's not. It's a property of the bonds. Nearly all force fields (if not
all of them) constrain X-H bonds at minimum, to remove the fastest motions in
the system and allow for a longer time step. Using dt on the same order as the
fastest frequencies leads to instability. See manual section 6.7.
> Could someone please let me know what the bond constraint requirements are
> for OPLS-AA and GROMOS forcefields (I'm going to need to use that next). I
> can't seem to find this information by searching but imagine its on a website
Information like this should be in the primary literature for the parameter
sets. I don't know of any sort of database online that tracks such things, and
moreover there are no absolute rules AFAIK. I generally follow the methods of
the paper that derived the parameter set. Unfortunately, sometimes they don't
say. For Gromos96 53A5/53A6, validation simulations were carried out with all
Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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