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Article ID: 910 - Last Modified:

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:

  1. Save your newly built protein-membrane system in a CMS file (referred to here as protein-membrane.cms.)
  2. Run the script to prepare the necessary input files:
    $SCHRODINGER/run -i protein-membrane.cms -t temperature -j protein-membrane
  3. 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

The relaxation protocol cannot be run on a GPU, so you must run it on a CPU. The protocol must be run from the command line with the steps given above. In particular, you must run the script in step 2 to prepare files for step 3; you cannot use input files written by Maestro.

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