While our lab generally uses NAMD for our simulations of transmembrane proteins, we are interested in testing out Amber11 on a Nvidia GPU using the Charmm class of force-fields. Searching through the list archive, there are several posts suggesting issues with Amber's ability to handle membrane simulations. I was hoping that members of the list with experience in simulating protein/membrane systems using Amber could comment on potential pitfalls moving a membrane system from NAMD to Amber. Obviously the barostats are different, and it seems like NAMD allows additional pressure controls absent in Amber. Additionally, if we are using the same force-field (charmm 27 w/CMAP corrections) that we used in NAMD, is it safe to transfer the coordinates of our pre-equilibrated system (from previous runs in NAMD) in a hexagonal cell to Amber, do a brief minimization and heating and then start a production run, or would you recommend rebuilding the system from scratch and doing a multi-tiered restrained equilibration?
Thank you in advance for any suggestions/insight you can provide.
Josh
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Dr. Joshua L. Adelman
Department of Biological Sciences
University of Pittsburgh, Pittsburgh, PA
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Received on Sat Oct 23 2010 - 08:00:02 PDT
