[gmx-users] Normal Mode Analysis

[Adip Jhaveri]

Hello All,
I am simulating two proteins in solution and would like to perform Normal
Mode Analysis on trajectory snapshots.

I take one particular frame in the trajectory and minimize it, followed by
mdrun for normal mode analysis. However I am getting constraint errors in
each of the two steps -
1) In minimization it is recommended to use 'cg' method but this does not
work and it throws an error due to the constraints present in the system.
2) I tried using the 'steep' method for minimization but then, during the
normal mode mdrun, it is giving an error on constraints. How do I solve
this problem? Do I completely remove the constraints and then perform 'cg'
minimization and 'nm' mdrun?

Regards,
Adip