[gmx-users] Position restrained Dynamics

[nikhil damle]

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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