Metadynamics i-pi+PLUMED

[Sriram Vignesh AK]

Hi all,
I am trying to estimate quantum free energy barrier for an isomerization process using i-pi and plumed. It should be a double well with the barrier height for the reaction around 25 kcal/mol(~105 kJ/mol). So i am using the following plumed input.

# default units are LENGTH=nm ENERGY=kJ/mol TIME=ps

#MOLINFO STRUCTURE=rctnt_E.xyz
q: TORSION ATOMS=4,9,7,8 #H5-N3-C1-N2
mtd: METAD ARG=q PACE=20 SIGMA=0.35 HEIGHT=80.00 FILE=plumed/HILLS BIASFACTOR=100 TEMP=300 GRID_MIN=-pi GRID_MAX=pi

PRINT ARG=q  STRIDE=1 FILE=plumed/COLVAR
FLUSH STRIDE=1


I am applying a bias on the required dihedral (RC). The system is diffusing between the two barriers as expected - but the free energy profile is always dominated by either of the one well ( the well the trajectory is accessing at the time of calculating free energy gets more deeper).
How do I tackle this problem? I am attaching a photo of the free energy profile at 4 different times alone - one can see that initially it deepens the edge wells and then deepens the central well.

Thank you so much for the help

Regards,
Sriram

[Qinghua Liao]

Hello, 

For your metadynamcis, the pace is too small, the height is too huge, even BIASFACTOR might be too big.

Before running a metadynamics simulation, it is better go through some tutorials, read some papers.

(Surprised that the simulation was not crashed)

All the best,

Qinghua