Hi, I am looking to restart a simulation from NAMD to Gromacs using their initial system setup and apply a uniform electric field across it. I've been given NAMD files but cannot find a way to convert these files to a more typical .gro or .top file in gromacs. How would I go about converting these files?
Dear Hannah,
I couldn't found any such tool, but you can use the Python scripts to do this, but it would be so difficult for you. You can ask for and use your .pdb files to generate all files in gromacs.
Hannah Burton
Take your PDB and convert your force-field parameters into Gromacs readable format. I believe you must have all proteins residues your system in standard format. If you have any mismatching of parameters, you can take help of Swiss-param to convert into standard required format. Then generate parameters (topology + parameters) files using pdb2gmx.
Installing Gromacs will solve your problem.
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