Jose Pena

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Questions related from Jose Pena

Parameterizing proteins with CHARMM36 & getting "WARNING: There are no atom pairs for dispersion correction" - running a simulation in GROMACS 2019?

Using the pdb2gmx module, I separately parameterized two proteins (polymers), I used the topologies of both and joined them in a single topol.top file. I have minimized the energy and the gromacs...

16 September 2021 6,280 1 View

Parameterizing proteins with CHARMM36 & getting "WARNING: There are no atom pairs for dispersion correction" - running a simulation in GROMACS 2020?

Using the pdb2gmx module, I separately parameterized two proteins (polymers), I used the topologies of both and joined them in a single topol.top file. I have minimized the energy and the gromacs...

16 September 2021 9,769 1 View

If I have already taken steps to equilibrate the system, should they not be considered valid?

Parameterizing proteins with CHARMM36 and getting the error "WARNING: There are no atom pairs for dispersion correction" when running a simulation in GROMACS 2020. Using the pdb2gmx module, I...

16 September 2021 9,912 2 View