Understanding hexane_cg.xml file in tutorials
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Satyen Dhamankar
Aug 30, 2021, 6:11:45 PM8/30/21
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I am looking at the hexane_cg.xml file in the tutorials, and I see that
bead A1, B, and A2 have the same mapping called UNITY, and the weights assigned to that mapping is simply 1.
I dont understand how this works. In the simple hexane.xml file, I have to write down every single atom that corresponds to that bead, make sure I am assigning the right weight to each atom, and give it a particular name. My question is, why, when performing the CG potential optimization, it is the same mapping, and the weight is given as 1? For example, since beads A and B have different masses, I would expect you to have different maps, like you have in the original hexane.xml file.
If I had a molecule which I have CG'd to beads A, B, C, D. For my molecule_cg.xml file for ibi, will I do the same thing as you have done in this example? Where the mappings have the same name?
I would appreciate any advice you have for me!
Christoph Junghans
Aug 30, 2021, 6:19:25 PM8/30/21
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On Mon, Aug 30, 2021 at 4:11 PM Satyen Dhamankar <saty...@gmail.com> wrote:
>
> I am looking at the hexane_cg.xml file in the tutorials, and I see that
> bead A1, B, and A2 have the same mapping called UNITY, and the weights assigned to that mapping is simply 1.
>
> I dont understand how this works. In the simple hexane.xml file, I have to write down every single atom that corresponds to that bead, make sure I am assigning the right weight to each atom, and give it a particular name. My question is, why, when performing the CG potential optimization, it is the same mapping, and the weight is given as 1? For example, since beads A and B have different masses, I would expect you to have different maps, like you have in the original hexane.xml file.
When you do a run with csg_inverse the topology is already a
>
> I am looking at the hexane_cg.xml file in the tutorials, and I see that
> bead A1, B, and A2 have the same mapping called UNITY, and the weights assigned to that mapping is simply 1.
>
> I dont understand how this works. In the simple hexane.xml file, I have to write down every single atom that corresponds to that bead, make sure I am assigning the right weight to each atom, and give it a particular name. My question is, why, when performing the CG potential optimization, it is the same mapping, and the weight is given as 1? For example, since beads A and B have different masses, I would expect you to have different maps, like you have in the original hexane.xml file.
coarse-grained one, hence the mapping file is only needed to define
the bonds/angles and so it is only a simple 1:1 mapping. In contrast,
the hexane.xml is a mapping file from an automatic topology to a
coarse-grained one.
>
> If I had a molecule which I have CG'd to beads A, B, C, D. For my molecule_cg.xml file for ibi, will I do the same thing as you have done in this example? Where the mappings have the same name?
beds A, B, C & D, apply the UNITY mapping everywhere and just add the
cg_bonded section.
Christoph
>
> I would appreciate any advice you have for me!
>
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--
Christoph Junghans
Web: http://www.compphys.de
Satyen Dhamankar
Aug 30, 2021, 11:47:54 PM8/30/21
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Got it, thank you Christoph.
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