I am performing molecular dynamics simulation in GROMACS for a protein-ligand (Phytochemical) complex using GROMACS via Simlab (Online). Currently they provide only 50 ns simulation. I need 100 ns. So can I approach in that way--
like first doing 50 ns simulation. The will give the complex to me at 50th ns. Then using that 50th ns complex again for another 50 ns run.
Then during trajectory analysis combining the first 50 ns data with the second 50 ns data to make 100 ns trajectory. Is it possible??? Need suggestions from experts.
Thank you so much.
Sincerely-
Sunzid.
I think your second submission will be processed from scratch. Energy minimization, equilibrium, and production run will be excuted again. I don't think it will be accepted to do so, and the RMSD is expected to change at the start of the second 50-ns run.
You can extend the first 50 ns of run
https://manual.gromacs.org/current/user-guide/managing-simulations.html
This is an unavoidable problem in most online servers. I have another suggestion. Analyze the data of your first 50 ns of MD run. Cluster your complexes with a tool like TTClust to derive all the clusters. Choose the cluster that contains the most structures/ensembles and the least rmsd. Choose the representative frame of this cluster. Then make sure to dock the exact pose of the ligand in your docking site by rigid docking. Again run MD Simulation for the next 50 ns and continue the process. Although it might ultimately lead you to your final conclusion (a protein-ligand complex stable for 50 ns) the drawback is you may have to present your paper as an MD simulation work with an MD run of only 50 ns even though you might have run your simulation many times over (i.e n*50 ns). Also, make it a necessary point to write this methodology in detail to convince the reviewers. Hope that helps.
Thanks Anshuman Sahu brother for your very nice suggestions, it has given me a new thinking to go. Thanks a lot.
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