Partial charges in the coarse-grained model
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Victor Nazarychev
Sep 30, 2022, 7:28:25 AM9/30/22
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Dear VOTCA users and developers,
I am trying to simulate polymers using Gromacs with CG models that were created by VOTCA. In my topology, each CG bead has zero partial charges. However, is it possible to introduce the charges in the CG topology by recalculating the partial charges for the atomistic model?
I have found an approach to introduce charges into a coarse-grained model using the RESPAC algorithm https://pubs.acs.org/doi/abs/10.1021/ct4007162 by recalculating the charge of a CG bead from the electrostatic potential of atoms that are coarsed in this CG bead. Is it possible to incorporate charges into a CG model using VOTCA, while considering the partial charges of the atomistic model? For example, by summarizing all the partial charges of the atoms that are coarsed in the atomistic model and assigning this charge to a CG bead, would this cause an error? Does VOTСA has an algorithm for calculating the charges of a coarse-grained bead?
Sincerely yours,
Victor
I am trying to simulate polymers using Gromacs with CG models that were created by VOTCA. In my topology, each CG bead has zero partial charges. However, is it possible to introduce the charges in the CG topology by recalculating the partial charges for the atomistic model?
I have found an approach to introduce charges into a coarse-grained model using the RESPAC algorithm https://pubs.acs.org/doi/abs/10.1021/ct4007162 by recalculating the charge of a CG bead from the electrostatic potential of atoms that are coarsed in this CG bead. Is it possible to incorporate charges into a CG model using VOTCA, while considering the partial charges of the atomistic model? For example, by summarizing all the partial charges of the atoms that are coarsed in the atomistic model and assigning this charge to a CG bead, would this cause an error? Does VOTСA has an algorithm for calculating the charges of a coarse-grained bead?
Sincerely yours,
Victor
Christoph Junghans
Sep 30, 2022, 12:11:49 PM9/30/22
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do coarse-graining of charged systems, but you are mostly on your own.
If you are looking through the archive of this mailing list, you will
have a couple of attempts to do that.
In short, you will have to figure out how to set up the coulomb
interaction and then you can do "normal" coarse-graining, e.g. like
IBI, on top.
Christoph
>
> Sincerely yours,
>
> Victor
>
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Christoph Junghans
Web: http://www.compphys.de
Victor Nazarychev
Oct 27, 2022, 5:39:23 AM10/27/22
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Dear Christoph,
Thank you very much for your help.
Best regards,
Victor
Thank you very much for your help.
Best regards,
Victor
пятница, 30 сентября 2022 г. в 19:11:49 UTC+3, Christoph Junghans:
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