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Align Principal Axes of the system to the coordinate axes prior to solvation #139

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cespos opened this issue Jul 17, 2023 · 1 comment · Fixed by #143
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Align Principal Axes of the system to the coordinate axes prior to solvation #139

cespos opened this issue Jul 17, 2023 · 1 comment · Fixed by #143
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enhancement New feature or request

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@cespos
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cespos commented Jul 17, 2023

Is your feature request related to a problem? Please describe.
The principal axes of the system are not aligned to the coordinate axes prior to the box generation and solvation.
It would be great to have the option (maybe for the BSS.Solvent.solvate function) to perform the alignment prior to solvation.

Describe the solution you'd like
This can be done with the gromacs command:
gmx editconf -f input.gro -princ

or with leap using the commands:
system = loadPdb input.pdb
center system
alignAxes system

Describe alternatives you've considered
I cannot see other alternatives. I think that the gromacs command line would be easier to implement also because BSS already uses gromacs for solvation.

@lohedges lohedges added the enhancement New feature or request label Jul 24, 2023
@lohedges
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Thanks for this suggestion. It would be easy to add this as an option to BioSimSpace.Solvent.solvate (and associated convenience functions).

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