Is there a specific equilibration protocol for membrane proteins in Desmond?

Yes. An .msj file has been developed specifically for equilibrating membrane proteins. It can be found in:

$SCHRODINGER/mmshare-vversion/data/desmond/desmond_membrane_relax.msj

You should copy and edit the file to change all the instances of $TEMPERATURE to the target temperature. Then the equilibration can be run from the Desmond MD GUI by selecting "Relax model system before simulation" and browsing to the location of the .msj file.

Keywords: mulitsim, equilibration, membrane protein, relaxation, msj

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