I am going to conduct molecular dynamics analysis of the protein-ligand complex in a Computer-Aided Drug Design project.
Hi,
Personally, I suggest using NAMD for running simulations. It allows you to use CHARMM forcefields, and you can use the associated VMD program for preparing the simulations.
You can use NAMD. I find you have to prewrite the files with the parameters you want to use in NAMD. In NAMD, there is some graphical interface that writes the files for you. You could also use Gromacs which gives you more command line control. If you are rich you can use AMBER.
Something I wasted a few months on was if you call the program from the command line on your PDB file and redirect it into the background with "&> output file", the program will never run on a university scheduler. But that actually works on a home computer. Don't use the "&" sign.
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