normal multiscaling

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4 years 3 months ago - 4 years 3 months ago #4050 by nanogod
nanogod created the topic: multiscaling
Hi,

Does anybody know if it is possible to make a multiscaled MD simulation with a CG protein except for a Cys residue, which should be ab initio calculated so that the Cys-Cys binding could be monitored in a self-assembly process?

Kind regards
Morten
Last Edit: 4 years 3 months ago by nanogod.

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4 years 3 months ago #4051 by mnmelo
mnmelo replied the topic: multiscaling
Hi

While conceptually it should be feasible to add more layers on top of an ONIOM approach, I am not aware of any such a CG-AA-QM implementation. Also, if you're talking about self assembly youl'll probably want both contact Cys to be described at the QM level, which raises the question of how to spatially and dynamically define the layering.

To make this all the more interesting (read, difficult) water interactions are probably important to your system. Having them cross resolution barriers can pose many challenges, even without going into QM (check our work on it [url=doi://10.1021/ct5001523]here[/url]).

All in all I think it'd make a nice PhD project. Do let us know if you succeed!
Manel

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1 month 1 week ago #7926 by peterkroon
peterkroon replied the topic: multiscaling
@molashahimaryam spamming the forums with the same question over and over will not make us help you, and in the worst case, gets you banned from these forums.
To answer: do some of the tutorials on this website.

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1 month 3 days ago #7934 by peterkroon
peterkroon replied the topic: multiscaling
You were.
On this forum we take precious time away from our own research and lives in order to help people. People who are disrepectful and do not appreciate the time and effort we invest we choose not to help. This means we expect people to invest a minimum of effort in the first place: clearly explain what their problem/question is, what they've tried, and what problems they encountered. This also includes independently doing some research into what's going on/how to use Martini beforehand. This means doing the tutorials, and reading the Martini papers. On top of that, it is polite (to say the least) to only post a single question once. It also costs us time to read them.
Since you've done *none* of those things you were temporarily banned.

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1 week 2 days ago #7949 by Sharif
Sharif replied the topic: multiscaling
Hi
How can I make itp file for an anion likes the TFSI anion in Martini ? How to obtain angle bonds, dihedral angle, bond length, ...?
I have searched a lot, but it seems there is not paper for the matter!
Thanks

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3 days 14 hours ago #7969 by riccardo
riccardo replied the topic: multiscaling
Hi Sharif,

I do not see how this question fits in this thread. Can you search through the forum and for a more appropriate thread or open a new thread in some more appropriate section (probably "Force field>Other Molecules")? Thanks.

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