[gmx-users] structure expanding beyond eq values

Nash, Anthony a.nash at ucl.ac.uk
Wed Feb 24 11:30:10 CET 2016

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

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.

Many thanks

Dr Anthony Nash
Department of Chemistry
University College London

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