Accelerated MD with transmembrane protein

From: Alison de Sousa Rebouças (alisonreboucas_at_gmail.com)
Date: Tue Sep 17 2019 - 13:48:46 CDT

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Hello, all!

I have a transmembrane protein with 4 helices and 2 extracellular loops
interacting with an antibody and I want to submit it to Accelerated MD
(aMD). There is any specific parameters to this kind of aMD simulation? Is
it possible to accelerate just the membrane dihedrals and not the
protein's? How can I do this?

I saw this parameters below, but I think they are just to accelerate
protein in aqueous solution, right?

# Accelerated Molecular Dynamics
# Edihe= <dihedral energy from standard simulation>
# Ecut = <dihedral energy from standard simulation> + 4*number of residues
that contains dihedrals
# alpha = (1/5)*4*number of residues that contains dihedrals
accelMD on
accelMDdihe on
accelMDE Ecut
accelMDalpha alpha
accelMDFirstStep $ftstep
accelMDLastStep [ expr $ftstep + $run ]
accelMDOutFreq $freq

Thanks in advance,
Alison.

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