[gmx-users] Position Restraints MD

[ISHRAT JAHAN]

 Dear all,
I am doing MD simulation of protein and metal atom. I had applied position
restraints on metal atom. I had applied it as follows- ( kindly correct me
if i am wrong)
first made an index of metal atom and generated the posre_ion.itp file
using gmx genrestr and then added the force and atom index into the top
file of protein in [position restraint] part. In full.mdp file , added the
line define= -DPOSRES.
Then performed full md. But when i calculated the rmsd of backbone its
value is found to be around 0.02 nm(very small). I do not know whether
restraints have been applied on metal or on the whole system.  Am I doing
it correct or not?
Any help related to this will be appreciated.
Thanks in advance


-- 
Ishrat Jahan
Research Scholar
Department Of Chemistry
A.M.U Aligarh