What time scale would be sufficient to show protein ligand interaction that we normally depict using molecular docking simulations. In addition what ensembles to use NVE or NPT while performing MD simulations?
Hi Lokesh,
As Sergey already suggested the time scale, but for better understanding check the fluctuations in the Ligand-protein system i.e. calculating the RMSD which will give you more insight about when to terminate your simulations to save time and have enough statistics to say your ligand-protein system.
Regarding the query about NVE or NPT, here is the link http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
go through with it and you will understand the parameters required to simulate your system. To be more specific they are using NVT and NPT.
Cheers!!
Currently, the standard time scale for the MD simulation of any protein-ligand system is in the range from 15 (20) to 50 (100) ns. However, the 50-100 ns trajectory file would occupy up to 1-2 TB of space depending on the size of the simulated system.
Hi Lokesh,
As Sergey already suggested the time scale, but for better understanding check the fluctuations in the Ligand-protein system i.e. calculating the RMSD which will give you more insight about when to terminate your simulations to save time and have enough statistics to say your ligand-protein system.
Regarding the query about NVE or NPT, here is the link http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
go through with it and you will understand the parameters required to simulate your system. To be more specific they are using NVT and NPT.
Cheers!!
Hi Lokesh, there is not a definitive answer to your question. First your protein has a metal catalytic site? If yes the protocol that you should follow is intricate.
If your model is without metal coordination you must use as target for the timescale the RMSD, as suggested by Anupam, taking in consideration for example the protein backbone. Regarding the ensembles usually NPT is the standard one.
Best
Paolo
Dear Friends, Anupam and Paolo, When You say RMSD please explian how that is related to timescale? To be specific if a start a MD simulation with time step of 2 fs ansd calculate rmsd differences at the interval of 0.5 ps till what rmsd value I should run the calculations??? say for example till 1ns I find that there is no substantial change in rmsd value between initial and 1ns conformation should I stop MD simulation at that time??? Please answer
Lokesh, I think you are right. But can't confirm you as i'm not an expert. Please consult the experts.
1ns is not enough to appreciate a conformational mutation. As Sergey suggested you need to punch your simulation at least until 10-20ns and then evaluate the RMSD. Keep in mind that you must monitoring the energy fluctuation: an equilibrated sistem has no energy fluctuation in a percettibile timescale.
Best
Paolo
- Badges
- Science topic
- Similar topics
- Chemistry
- Theoretical Chemistry
- Computational Chemistry
- Molecular Dynamics