Hi All,
I am trying to simulate kinase domain (chain A) in complex with cyclin (chain
B). During solvent dynamics, PBC on and PME treatment of electrostatics, i need
to keep only kinase domain flexible but cyclin fixed.
i put POSRES_B in define variable and tried to simulated the entire solvated
system in GROMACS 4 package. But time and again it failed with LINCS warnings.
On the contrary, if entire system is kept either flexible or position
restrained, run is obtained without any errors. I tried 1ns MD. Unable to
understand possible reasons.
Could anybody help in this regard ?
Regards,
Nikhil
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