Hello researchers,
I was wondering what is the difference between energy minimization on Pymol versus using mdrun module on Gromacs MD package. Is it just more forcefield options on gromacs?
Thank you,
Neena
PyMol only does only very rudimentary energy minimization. Optimize is a PlugIn that lets you access some of the energy minimization options of OpenBabel https://pymolwiki.org/index.php/Optimize. But it's no comparison to programs whose core competence is based correct assessment of molecular energies and the forces exerted by intra- and intermolecular interactions, such as molecular dynamics and molecular design applications.
PyMol only does only very rudimentary energy minimization. Optimize is a PlugIn that lets you access some of the energy minimization options of OpenBabel https://pymolwiki.org/index.php/Optimize. But it's no comparison to programs whose core competence is based correct assessment of molecular energies and the forces exerted by intra- and intermolecular interactions, such as molecular dynamics and molecular design applications.
All of them are supposed that stabilize the atoms respect to other neighborhood atoms in an unreal world - so they shouldn't be taken serious.
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