[gmx-users] Hydrophobic contact cut-off

[Christopher Neale]

The standard approach in cases like this, assuming that you have some contacts at some point in your trajectory, is to use your trajectory to construct a radial distribution function (RDF) and then to define a "contact" as any interaction up to the minimum following the first maximum of the RDF. This way, your cutoff will depend on your definition for contact evaluation (any atom pair, heavy atom pair, side chain center of mass, etc).

Chris.

-- original message --

Sorry for an off-topic question..

What is the distance cut-off considered for
hydrophobic contact in protein?
Some paper states 4-8Ang, while some other
considers only till 5Ang. It is reported that this
is a long range interaction.

Any information clarifying this doubt will be very
useful.

Thank you
Kavya