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

From: I. Camps (
Date: Thu Mar 03 2022 - 13:46:30 CST

Dear Giacomo,

Thank you very much for your suggestions.

My systems are ready. I created (and functionalized) them using other
tools. Also, I study them with DFT and semi-empirical methods. The ones
created by VMD are, let said, not useful.

Now, I want to create bigger systems where they will work as nanofilters,
so I need to add a solvent and the small molecules (greenhouse gases,
pesticides, among others)



On Thu, Mar 3, 2022 at 1:52 PM Giacomo Fiorin <>

> 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:
> 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
> hand.
> 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.
> Giacomo
> 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

This archive was generated by hypermail 2.1.6 : Tue Dec 13 2022 - 14:32:44 CST