Generating topology files for crystalline materials

From: FX (
Date: Sun Feb 10 2013 - 12:05:26 CST

Dear NAMD list,

I'm trying to get a NAMD simulation running for an organic-inorganic crystalline material. I already have a forcefield for my system, and already run some MD using other codes. I'm now trying to create inputs file for an NAMD simulation, but I am at loss how to create the topology file. I've read the tutorials (both the generic tutorial and the advanced "topology files" tutorial), but they only cover biological systems made of a series of residues.

In my case, the entire unit cell is made of only one molecule, extending in 3D through periodic boundary conditions. So, I'm wondering: what is the procedure I should follow to create this topology file?

Thanks in advance for any help or resource you can point me to!

François-Xavier Coudert

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