Re: << Tool to create NAMD input for non biological system >>

From: Giacomo Fiorin (
Date: Thu Mar 03 2022 - 10:52:00 CST

For generating the topology, I think it really depends on the specifics of
what you're trying to model, and with what force fields. You can already
generate C-C and B-N nanotubes and sheets within VMD (I checked the
nanotube builder included in version 1.9.4, I don't use 1.9.3 any more).
But functionalization will require additional work. You could look into
the Tcl code of the nanotube builder plugin to see how it's done.

You can also TopoTools to modify an existing system, e.g. adding bonds,
angles and dihedrals between atoms that could allow you to save a PSF file
from VMD:;!!DZ3fjg!phbO43UcJB31pvWmwHfdV1-JIvFnO8UhF2xpXDeiOVo80uCC2fS4DhX7NEjK7l8gyA$
This is distinct from psfgen, which also runs in VMD but has its own
separate memory space.

Comparing with previous messages from you, it seems that you may be also
looking for a code to write out your NAMD script in full. But using an
input generator is primarily useful in two cases: (1) in the learning
phase, when one is just beginning and may be overwhelmed by too much
complexity in a limited time (e.g. a summer intern), or (2) in production,
as a way to automate tasks that you would otherwise know how to do well by

I really think you should first find out each and all of the steps that you
need to realize the kind of simulation you need, and only after that look
for resources that automate the process and save yourself time.


On Wed, Mar 2, 2022 at 8:46 PM I. Camps <> wrote:

> Hello,
> I want to run molecular dynamics simulations for non biological systems
> like carbon nanotubes (pristine and functionalized with -OH and/or -COOH)
> interacting with small molecules.
> Is there a way to generate the NAMD input files?
> I already tried VMD and CHARMM-GUI unsuccessfully.
> Best regards,
> Camps

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