Re: Generating topology files for crystalline materials

From: FX (
Date: Sun Feb 10 2013 - 14:02:16 CST


Thanks for the help. (You're on the CPMD, VMD, NAMD lists… do you watch all the ".*MD" lists? :)

> the molfile plugin API now also supports writing out topology
> information, so you can generate the topology information from VMD
> scripting. this can be tedious and error prone, so it would be
> beneficial to write some scripted tools for that. the topotools
> plugin, for example provides a "middleware" that can automate a large
> part of the process. check out:

If I "only" need to generate a list of bonds

> you'll have to come up with a smart way to add the bonds that wrap
> around periodic boundaries

Shoot. I was expecting this to be available in NAMD directly, not to have to reinvent it. Are there never bonds that wrap around the unit cell? I'm sure at least someone has simulated zeolites, fully flexible polymers, something like that...

> and i would be curious to learn, if the
> automatic derivation of topological angles and dihedrals will work
> correctly in those cases (never had a chance to try it on a real world
> problem).

Well, the publication whose results I am trying to reproduce says simulations were run using NAMD, so it appears to work :)

> it may be simpler to build the topology information direction, since
> you know your structure and i assume there are some simple rules to
> follow.

I searched for "topology information direction" in the doc, tutorials, and pretty much anywhere in Google, but nothing turns up. What do you mean?

If it's a sort of "automatic topology" feature (like Gromacs or GULP has, where I can give a list of rules like "type N1 is any N atom linked to C, C and H", then yeah, I have simple rules I can feed it. How can I access it?

Thanks again,
FX Coudert

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