[gmx-users] structure expanding beyond eq values

Justin Lemkul jalemkul at vt.edu
Wed Feb 24 15:49:59 CET 2016

On 2/24/16 5:30 AM, Nash, Anthony wrote:
> Hi all,
> Any thoughts on what could be causing my structure to expand and distort
> well beyond (about 2 to 3 angstrom with some distorted angles) the
> equilibrium bond lengths during energy minimisation?
> I¹ve fully parameterised two new fragments, which include new atom types
> and force constants. The first fragment (sitting between two glycine
> residues) behaves very well. The second fragment (separate simulation
> altogether, similar set up, only difference is an added ethane group to
> the central ring of the fragment) doesn¹t get past the energy minimum
> stage.
> As an example on bond length force constants:
> Fragment #1
> MC7 MN4 1 0.146 86531.610
> Fragment #2
> GC11 GN3 1 0.145 57828.550
> This bond is from the same part of a circular structure, the only
> difference is a functional group elsewhere in the ring. That particular
> bond in fragment #2 goes from 0.145 to 0.3 angstrom. I¹ve tried putting
> the initial structure, and the broken-minimised structure, into an NVT but
> it results in LINCS errors.
> Note: the initial structure came from a HF/6-31G(d) optimisation.

Then you likely have a problem elsewhere.  Conduct a single-point energy 
evaluation to make sure everything is sensible.



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


More information about the gromacs.org_gmx-users mailing list