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AMBER Archive (2009)Subject: RE: [AMBER] Umbrella Sampling
From: Seetin, Matthew (Matthew_Seetin_at_URMC.Rochester.edu)
Alternatively, you can ignore the iat variables and define the restraint as follows:
restraint="distance(com(:[residue]@[atom name],...), com([atom numbers of molecule]) )
Omitting the brackets and supplying the residue numbers, atom names, and atom numbers as appropriate. There are further examples and clarification of this more human-readable scheme in section 6.1 of the manual should you find this a little easier.
--Matt Seetin
-----Original Message-----
> I want to calculate free energy change during the process of insertion of
To have a coordinate that is the center of geometry of several atoms, set
Don't use too many atoms in igr1, or things may become unstable. You may have
....dac
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