Re: Generating topology files for crystalline materials

From: FX (
Date: Sun Feb 10 2013 - 15:58:31 CST

> this really is not a NAMD issue. NAMD just uses the bonding
> information provided in the psf file and PBC treatment will make it
> irrelevant whether bonds wrap around boundaries or not.

OK, perfect. Sorry I misunderstood.

As you say, it seems the best solution for me is to write the psf file from my own scripts. I already have this sort of stuff in place, because I use it for post-processing the trajectories.

> i'm not talking about NAMD, but the topotools Tcl code.

OK, misunderstanding on my side again.

>> I searched for "topology information direction" in the doc, tutorials, and pretty much anywhere in Google, but nothing turns up. What do you mean?
> damn autocompletion. "direction" was supposed to be "directly".

Yeah, then that's what I'll do.

One final (I hope) question: is the list of bonds and dihedral required in the psf file, or can NAMD rebuild it itself? I ask because it could save me time to only write bonds and improper dihedrals.


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