Article ID: 910 - Last Modified: October 24, 2013
Is there a specific equilibration protocol for membrane proteins in Desmond?
Yes. This protocol is documented in section 3.8, "Simulations on Systems with Membranes" of the Desmond User Manual.
To use the membrane relaxation protocol:
- Save your newly built protein-membrane system in a CMS file (referred to here as protein-membrane.cms.)
- Run the script to prepare the necessary input files:
$SCHRODINGER/run relax_membrane.py -i protein-membrane.cms -t temperature -j protein-membrane
- Run the membrane relaxation protocol using the command
$SCHRODINGER/utilities/multisim -JOBNAME protein-membrane -HOST myhost -mode umbrella -cpu cpus -i protein-membrane-in.cms -m protein-membrane.msj -o protein-membrane-out.cms
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