I used namdenergy plugin in vmd to extract total, vdw and electrostatic energy. I am confused to know about the energy provided by apbs/mmpbsa. How it is different from the data obtained from namdenergy. I had performed md in namd and would prefer to use namd for energy calculations. Any suggestion would be helpful to understand this more clearly.
@Elvis thanks for your explanation, how about first part of my question "How it is different from the data obtained from namdenergy."
Thanks Elvis, for the reply, that means namdenergy = MM + MMPBSA/GBSA. How about electrostatic energy we obtained from namdenergy calculations.
Elvis, thanks again for reply. Some more questions I have, I want to calculate the interaction energy between protein adsorbed on graphene surface, and I was wondering to calculate the namdenergy for interaction and electrostatic calculations. I think using APBS would be better choice for energy between two molecules. DO you have any suggestion for this.
- Badges
- Science topic