[gmx-users] Simulation membrane proteins in amber99 force field.

[Christopher Neale]

Dear James:

As always, check the primary literature. The Amber99SB ff was introduced with an 8A cutoff and PME: http://www.ncbi.nlm.nih.gov/pubmed/16981200

Other cutoffs are at your discretion. I am, for instance, using this ff with a 1.0 nm cutoff and PME because I am using it with the Stockholm Lipids.

Chris.

-- original message --

I'd like to perform MD simulation of the membrane protein parametrized
in Amber99sb force field. Could you tell me what cut-off patterns
should I use for such simulation ?


James