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Update for USER-CGDNA package #1573

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merged 6 commits into from Jul 19, 2019

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@ohenrich
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commented Jul 19, 2019

Summary

This pull request comprises one bug fix and one enhancement. The bug fix is related to a wrong increment of the virial in all bond_oxdna and pair_oxdna styles. The enhancement allows now to set the temperature dependence of the stacking strength from the input file. This made the pair_oxdna2_stk style redundant and was done in preparation for the future implementation of the oxRNA coarse-grained model for RNA.

Author(s)

Oliver Henrich, University of Strathclyde, Glasgow

Licensing

By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).

Backward Compatibility

The setting of the temperature dependence of the stacking strength from the input file breaks backward compatibility. In the command that sets the pair coefficient, e.g. for oxDNA2

pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65

two additional input fields appear now behind the temperature setting (${T} in the above example). This has been done to limit the number of hard-coded dependencies (now only the geometry of the nucleotide) and in preparation for the implementation of the oxRNA model.

Implementation Notes

The changes were verified using the same benchmark tests as before. Apart from numerical noise there is no difference in the results for e.g. kinetic energy of rotation and translation, potential energy and total energy. The value of the virial tensor has been verified against the results obtained with the oxDNA standalone code (https://dna.physics.ox.ac.uk).

Post Submission Checklist

  • The feature has been verified to work with the CMake based build system

Further Information, Files, and Links

All documentation, etc has been updated to reflect the changes in the input files. A new example 3 has been added that allows to compare time-dependent observables directly with the oxDNA standalone code, which uses a different mass and moment of inertia of the nucleotides.

@ohenrich
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I, the author, reviewed all these changes.

@akohlmey akohlmey changed the title User cgdna Update for USER-CGDNA package Jul 19, 2019

@akohlmey akohlmey self-assigned this Jul 19, 2019

@akohlmey akohlmey added this to the Stable Release Summer 2019 milestone Jul 19, 2019

@akohlmey akohlmey requested review from athomps, sjplimp and stanmoore1 Jul 19, 2019

@akohlmey akohlmey merged commit 67b74ae into lammps:master Jul 19, 2019

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