Dear Matias,
Thank you very much for your reply and I’m sorry for the cryptic question.
I am essentially working on the implementation of a rather new version of the Glycam force field, which is described here: https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.6b00295 <https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.6b00295> . The strategy there is basically changing the epsilon values for some of the atom types while keeping the original 1-4 interactions intact (Sec. 4.2.2). So basically, vdW and Coulomb energy terms will be modified while 1-4 vdW and 1-4 Coulomb terms will remain the same.
By using Parmed’s “addLJType” (as well as with changeLJType, got the same results) I make the modifications to the epsilon values. These modifications change the vdW energy values as well as the 1-4 vdW energies that I obtain from a single-step minimization, which I think is expected. However, to be consistent with the above proposed force field, I need to keep the 1-4 interactions the same. For instance, changing the sigma/epsilon values for a given atom type at the [atomtypes] directive in Gromacs does not alter the calculated 1-4 interactions. I was wondering if the same functionality exists in Amber.
I cannot use changeLJ14Pair or similar commands because I obtain the topology using leap not with chamber.
best,
Batuhan
> On 21 Oct 2020, at 20:25, Matias Machado <mmachado.pasteur.edu.uy> wrote:
>
> Dear Batuhan,
>
> I don't fully understand your question...
>
> The 1-4 LJ terms are the result of scaling the resulting LJ pair interaction by the SCNB factor.
>
> If you want to set new LJ parameters to each type, then look at keyword "changeLJSingleType". This will reset all corresponding LJ pair interactions (including 1-4 if any). To preserve the former 1-4 values, you can then use the keyword "changeLJ14Pair" to revert the previous effect on specific 1-4 LJ interactions (Note: it only works in chamber-created topologies, I've never used).
>
> If you want to set particular LJ pair paramters out of the combination rule but not to change the LJ of the type, then use keyword "changeLJPair". Only the LJ parameters of the selected pairs are affected (including 1-4 teres if any). Again, use keyword "changeLJ14Pair" to revert the effect on the 1-4 interactions.
>
> Best,
>
> Matias
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "Batuhan Kav" <bkavlist.gmail.com>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Lunes, 19 de Octubre 2020 12:23:32
> Asunto: [AMBER] Changing lj_radius without changing lj_14_radius
>
> Dear All,
>
> In my system, I’m trying to change the LJ parameters of certain atom types using Parmed’s addLJType command. However, while doing this I need to keep the 1-4 interactions unchanged. I’ve realized that, when I change the LJ radius/epsilon using the addLJType command, the 1-4 vdW energy (as the minimization output suggests) also changes and the radius_14 option in Parmed is only for the chamber-related topologies.
>
> Is there any way to accomplish this?
>
> thank you alll,
> Batuhan
>
>
>
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Received on Thu Oct 22 2020 - 02:00:02 PDT
