Hello,
I wanted to know how can I minimize the standard deviation (SD) of my simulated protein-ligand complex of 50ns using MM/PBSA method of Cafe 2.0 plugin of VMD plugin using NAMD. I have tried number of different ways- like decreasing the number of frames from 2000 to 250 and even adjusting the internal dielectric (pb_indi) constant value at 1, 2 and 4. However, in each indi values, I got a higher SD value 4.57, 20.13, and 30.12 respectively. However, with the pb_indi value as 1, resulted in lower binding energy i.e. -5.49 kcal/mol.
Are there any other ways that I can minimize the SD as well as get a higher negative binding energy?
Thank you for consideration.
Increase the number of frames by several orders of magnitude. For reference, linear interaction energy (LIE) approach uses millions of snapshots and takes into account explicit solvent . . .
- Badges
- Science topic
- Similar topics
- Computer Communications (Networks)
- Simulators