On 4/03/2010 10:15 PM, Ajeeta kaushiki wrote:
Dear Sir
I am doing a coarse grain MD of a membrane protein using Martini force
field and parameters . In course I am facing problem in understanding "
how the harmonic restraints will be applied to mimic secondary structure
H- Bonds of the atomic structure to the coarse grain model to maintain
secondary structure element " . Is this will be specified in the 'mdp'
file .
These might be applied in various ways - see chapters 4 and 5 of the
manual for some discussion.
Mark
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