Molecular dynamics
Hi,
I would like to perform metadynamics to a gpcr bound in a lipid bilayer to a protein ligand which I docked to the receptor. From a paper I know the structural differences between the active and inactive receptor.
From what I understand would be good practice to:
- Show that running unbiased MD does not show the activation of the GPCR.
- Run also the receptor without any ligand to show the energy difference with and without the ligand
- Run a negative control with a protein who supposedly does not activate the receptor
- Run the MD in triplicates.
Since keeping up with all these practices would mean a lot of computational power that since I am using my university HPC that implies a lot of queuing and stuff. How long should i run unbiased and meta md? Should i do triplicates? Is it really important to run a negative control?
And for the one experienced in metaMD, how do i pick a CV that makes sense? And other tips?