What will be the appropriate time scale or number of steps for membrane and a protein (73 amino acid long) for equilibration and production?
Lipid molecules move significantly over tens of nanoseconds or longer, which should help decide for the equilibration. But the time scales of the protein itself are entirely dependent on its conformational landscape. Nothing meaningful can be said there without knowing the details of your system.
Giacomo
Let me explain my work, so that it will be clear about the system.
I’m simulating a POPC membrane with varying concentration of ergosterol (1:0 1:0.2. 1:0.5 1:0.7 and 1:1( POPC: ergosterol )) with KMP-11 protein(73amino acids long,surface protein) of leishmania Donovani to look into molecular characterization of the interaction.
Can you me the time scale for equilibration and production?
Thankyou
Unfortunately the time scale of the relevant motions is not something that can be decided so quickly, the information you provided is still limited. Also, anything you observe in simulation will be affected by the initial configuration.
Without going into the details of your protocol (which is under your control and your coworkers’) I can constructively suggest to try a smaller/simpler peptide with known interaction with the membrane and test your protocol with it.
Ultimately this is a scientific question, not a GROMACS one (which could be answered more precisely). You won’t be able to get a more precise answer, unless the person replying has effectively taken over your project.
Giacomo
Following the tutorial given for gromacs I’ve equilibrated the system for 500ps and 1000 PS for npt and nvt respectively.
Will that work?
Also can you tell me what kind of details related to the the system that we are simulating to infer the time scale details?