Hello Everyone,
I have started coarse-grain modeling of protein structure using VMD. I have gone through the tutorial of residue-based coarse-graining procedure using VMD. My ultimate goal is to transfer the coarse grain coordinate and force field files into lammps formate.
1. Is there any protocol exists?
2. Is there any code to convert the topology and forcefield file to lammps data file?
Thank you!
Hi Khandakar,
I don't have the answers to your questions unfortunately, but have you considered running the simulations in NAMD? It would be easier, as you'd avoid having to convert everything to LAMMPS format
Hi Khandahar,
Similar as mentioned Patrick, I would recommend you to perform simulations with gromacs, so you would avoid having to convert between different formats, which then it could generate artifacts.
http://cgmartini.nl/index.php/tutorials
From my experience, VMD cgtool is great for creating martini proteins.
Check this tutorial
https://www.google.com/url?q=http://www.ks.uiuc.edu/Training/Tutorials/martini/rbcg-tutorial.pdf&sa=U&ved=2ahUKEwjF4vHpq_3lAhWJLlAKHZt6BTYQFjABegQIChAB&usg=AOvVaw1peftxh6Ao2L9P_tl2Gcfb
Then you can use any md engine you like. I've used lammps, with vmd topotools or the script ch2lmp.pl to convert.
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