Re: Free energy between two graphenes with WHAM
10/23/20 06:38 AM
Thanks to reply.
First, I didn't use the DOMDEC codes.
Second, the results seem to be that the restraints are well working by checking the configurations over time.
In my script, I just called/set the force fields/the crystal structure/the system information/nonbonded part before the restraint part.
Also, after the restraint part, there is the dynamics part.
I made 21 independent systems (windows) with the different distance (10~20 ang.) between two graphenes with 0.5 ang. interval.
The cylindrical restraints are just for making graphene impossible to translate with x, y-directions,
which means that the reaction coordinate in this system is only the z-direction distance between two graphenes.
The reason why I use the plane restraints, is that normal vector of the graphenes must be perpendicular (or close to) to xy-plane for my study.
My problem is that The free energy landscape looks good, but the free energy difference between local minimum and other regions (just 0.5 kcal/mol).
Do I need to product the number of atoms 88 (88 atoms in 1 graphene) to the free energy landscape? (if right, then the free energy scale is too large.)
Thank you to read my question.