From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Apr 10 2012 - 07:16:18 CDT
On Apr 10, 2012, at 7:38 AM, Ali Ghaffaari <ali.ghaffaari_at_gmail.com> wrote:
> I'm not skilled in MD. I have question about force field using NAMD. As I read in a NAMD documentation, it's using five potential energies: U(bond), U(angle), U(dihedral), U(vdW), and U(Coulomb). I want to simulate a protein by using a custom potential function for each atom rather than these five potential energies. How can I do that? Is it possible by using NAMD? or other MD tools?
To be able to properly do that you *first* have to become experienced in MD. It is not a matter of the tool, but a matter of understanding. Starting a project you don't understand is a recipe for disaster.
> Thanks a lot,
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