Positive energy (VDWAALS) in MMPBSA analysis

[Venu Battena]

My research on In silico analysis of drug targeting interactions on protein_drug and First I do docking with protein and ligand, the result of binding score is -10.73. An observe the amino acids of protein is attached to the ligand and after am moving to the MD Simulations using gromacs and run the simulation for 100ns with CHARMM36 force field and TIP3 water model. My results are RMSD, RMSF, Rg, SASA and Hbonds also good. But the MMPBSA of delta total energy is high positive (551.3) using the method gmx_mmpbsa and In this VWD energy is getting more positive. After am running the umbrella simulation for that complex (high positive MMPBSA value) but the binding energy is -9.7. Can you please help me to find out why MMPBSA value is high positive and how to solve this problem ?

Note : I run simulations for five complexes and four complexes of MMPBSA are -24, -21, -14 and -7 only fifth one is 551.3. Again am verified the MD Simulation method and gmx_MMPBSA setup. 

Thanks 

B.Venu

[marioe911116]

something doen'st feel rigth about the vdwaals results. Did you check the simulations for posibles unespected "jumps" due to PBC conditions? also, how does the vdwaals energy over time look like?