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Martini & gmx energy
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1 year 1 month ago - 1 year 1 month ago #9598
by peter
Martini & gmx energy was created by peter
Hey everyone,
I am facing an issue with my data analysis. I performed some molecular dynamics simulations with a few copies of ligands.
The simulations worked fine except for perhaps some bond rotation errors. Although sometimes the simulations stopped because of that, there were usually no issues for 100s of nanoseconds once they were restarted.
However, I just did some analysis using the "gmx energy" tool, but I noted that only the first ligand displayed any sort of interaction with the rest of the system.
I checked the relevant coordinate (.gro) files, and nothing seemed to be out of order. Moreover, no other errors were observed other than the one mentioned before. Furthermore, I am not sure if "gmx energy" can calculate the interactions for the Martini model correctly.
Please share some feedback regarding this if feasible. Thank you very much.
I am facing an issue with my data analysis. I performed some molecular dynamics simulations with a few copies of ligands.
The simulations worked fine except for perhaps some bond rotation errors. Although sometimes the simulations stopped because of that, there were usually no issues for 100s of nanoseconds once they were restarted.
However, I just did some analysis using the "gmx energy" tool, but I noted that only the first ligand displayed any sort of interaction with the rest of the system.
I checked the relevant coordinate (.gro) files, and nothing seemed to be out of order. Moreover, no other errors were observed other than the one mentioned before. Furthermore, I am not sure if "gmx energy" can calculate the interactions for the Martini model correctly.
Please share some feedback regarding this if feasible. Thank you very much.
Last edit: 1 year 1 month ago by peter.
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