Knowledge Base

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 relax_membrane.py -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 step3; you cannot use input files written by Maestro.

Back to Search Results

Was this information helpful?

What can we do to improve this information?


To ask a question or get help, please submit a support ticket or email us at help@schrodinger.com.
Knowledge Base Search

Type the words or phrases on which you would like to search, or click here to view a list of all
Knowledge Base articles