From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Mar 03 2022 - 14:02:57 CST
In that case, especially if you have a variety of solvents, the first thing
to do is to pick a suitable force field, and use the tools that support it.
Giacomo
On Thu, Mar 3, 2022 at 2:47 PM I. Camps <icamps_at_gmail.com> wrote:
> 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)
>
> []'s,
>
> Camps
>
>
> On Thu, Mar 3, 2022 at 1:52 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> 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:
>> https://urldefense.com/v3/__https://sites.google.com/site/akohlmey/software/topotools__;!!DZ3fjg!vMp3nFiz3HvYfR5xiCSePGTbldawD8PyUUCZlg8TXnQAbIRmlV_TujO4BsHFDOYYYg$
>> 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 <icamps_at_gmail.com> 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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