Hi, I'm using Gromacs 2020 for my simulations and I need to use some forcefield parameters published in the literature for calcite. The thing is that the paper I'm using gives force constants in k2 and k4 for improper dihedrals, with the function form E=(k2)(d^2)+(k4)(d^4), instead of the more common harmonic potential form. I have also checked all other improper dihedral functions Gromacs takes and it just seems this isn't available. Has anyone encountered this problem with Gromacs before and how do I solve it, if possible at all?
Hi,
are you referring to this article?
Article Experimental and molecular dynamic simulation study on calci...
On the SI you have all information about calcite parameters for MD. Then, you have several tools to convert LAMMPS to GROMACS:
https://stackoverflow.com/questions/51546719/is-there-any-way-to-convert-lammp-file-data-to-gromacs-files-top-and-gro-if-n
https://github.com/shirtsgroup/InterMol
You have also parameters for calcite in this article.
Article Molecular dynamics simulation of electrolyte solutions confi...
HI Ricardo, thank you for your answer. I'm using parameters from Article Derivation of an Accurate Force-Field for Simulating the Gro...
I don't need to convert the file format per se. It's just the improper dihedral parameters that are written in terms of distance (so with two force constants), but gromacs expects a harmonic type function with the parameters as one force constant and reference angle. I'm just wondering if there is a way of converting between the two functions forms.
Hi again,
I see your point. Well, in GROMACS you only have a limited set of improper dihedrals, aiming for keeping groups planar (as in aromatics) or for tetrahedral centers (not in OPLS). Depending on the forcefield you have Rickaert-Bellemans or Buckingham potentials. But one needs to now 1) which force field you are using, and 2) which type of improper you want to parameterize (planar groups or tetrahedral centers).
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