Messages

1

General Questions and Answers / Preventing the TremoloX builder from loading default potentials

« on: August 5, 2021, 18:55 »

Dear all,
Whenever I use the script generator to try to build a custom force field for a system with gold, carbon and sulfur the builder already loads two default reaxff potentials and I'm unable to find an option to delete them from the configuration. I want to add a custom one, not to use the default ones. However the custom one is added on top of the default ones and the builder never creates a blank potential set. How do I solve this?
Thanks,
Mattia Siviero

2

General Questions and Answers / Tremolox using multiple tags for the same particle

« on: July 28, 2021, 18:54 »

I'm noticing an issue I have with the tremolox potential builder: apparently I cannot have a particle with more than one tag. If I do I get the errror "the potential set is missing support for particle "x" with tags ['y','z'].
Now, why would there be such a problem?
Basically I have a ferrocene molecule. I used a unique tag for all the carbon atoms involved in the two ciclopentadiene rings. All the ring atoms are bonded to a dummy hydrogen atom in the center and to the adjacent carbon atom
However then I need to set the dihedral to constrain the rotation of the rings parallel to each other. To do that I need to select two specific atoms of the ring and fix the dihedral [carbon,dummy atom, dummy atom, carbon].
However the only way I see to select a specific atom for a force field term is to assign a separate tag to it and reference the (atom type, tag) combination. If an atom can only have one tag the process of setting all interactions I need becomes extremely tedious because then I have to respecify separately all force field terms involving the new atom so I'd assume I'm missing on something

3

General Questions and Answers / Re: Including additional potential classes into the tremolox potential set

« on: July 28, 2021, 00:15 »

Yeah, I hadn't thought of that simple solution for some reason.  Though in the end it was faster to just derive the coefficient with fft since I end up with a finite series anyway

4

General Questions and Answers / Re: MD: Deposit a molecule with a custom force field on gold.

« on: July 28, 2021, 00:09 »

Ok, everything is so much clearer now, thank you a lot

5

General Questions and Answers / Re: Including additional potential classes into the tremolox potential set

« on: July 27, 2021, 14:42 »

one term in particular is the one described in https://docs.lammps.org/dihedral_nharmonic.html, basically a series of cosine powers.
Another was a term I had derived from dft calculations which I decided to represent with a cubic spline interpolation (built in in lammps) because I couldn't find a good approximation with a fourier series (probably a problem with how I interpolated).

6

General Questions and Answers / Re: MD: Deposit a molecule with a custom force field on gold.

« on: July 27, 2021, 14:31 »

Thanks for the exhaustive reply.
I have to look into the templates because they seem quite the useful tool.
I still have to build it from scratch because ferrocene groups are pretty weird objects requiring for example dummy atoms to build a force field that's stable.
What I was missing is how bonds are assigned, especially the fact that I could tag atoms of the same type with different tags. There's a lot to unwrap here for me.
Another thing I'm wondering: is there a way to specify the partial charge for individual atoms? or do I have to tag them one by one?

By the way, I've gotten more than one error message of the type "The potential set is missing support for particle C with tags ['C_dih', 'C_fc']". Does it mean that I have bonds with unspecified bonded interactions?

7

General Questions and Answers / Including additional potential classes into the tremolox potential set

« on: July 26, 2021, 12:57 »

Hi,
is it possible to add new classes to the tremolox potential set as needed? I'm seeing that some dihedral interactions I need (cosine power series and fourier) are missing.

8

General Questions and Answers / MD: Deposit a molecule with a custom force field on gold.

« on: July 24, 2021, 14:22 »

I have a md simulation I performed on another software, lammps, which I want to recreate using quantum atk and which involves creating a gold substrate, adding to the simulation box a droplet consisting of thiolated ferrocene molecules molecule with a custom force field and then simulate the self assembly of this droplet on the gold substrate.

The thing is that I'm not finding an obvious way to add a determined number of molecules with a predefined force field to the simulation box. I can use packmol, but then the real problem for me is figuring out how to define the list of bonds, angles, dihedrals and impropers and nonbonded interaction in the molecule.
Can anybody direct me to some explanation that can clarify what the workflow is for the creation and deposition of complex biological molecules?
Thanks,
Mattia Siviero