[gmx-users] Position restrained Dynamics

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 10 15:49:10 CEST 2010

nikhil damle wrote:
> 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.

Probably by restraining whatever configuration you're starting with, you're 
preserving some unresolved clashes in the system.  By either restraining both 
chains or allowing both to move, you are overcoming the problem.

> Could anybody help in this regard ?

Watch the trajectory to see what's going on.  A few other general tips:



> Regards,
> Nikhil


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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