normal multiscaling

  • nanogod
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4 years 2 months ago - 4 years 2 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 2 months ago by nanogod.

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4 years 2 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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2 weeks 3 days ago #7885 by molashahi
molashahi replied the topic: multiscaling
Dear Experts
Would you tell me please how can I build accurate coordination file for PEO (100 monomer and bead C-C-O)?
Thanks

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1 week 3 days ago #7919 by molashahi
molashahi replied the topic: multiscaling
Dear Experts
How can I build coarse grained PDB file for PEO(100 monomers)?
Or how can I convert all-atom PDB file to Coarse grained PDB file?
Thank you very much

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1 week 2 days ago #7920 by molashahimaryam
molashahimaryam replied the topic: multiscaling
Dear Experts
How can I build topol.tpr and trajxtc file for forward mapping:

python indexer.py


seq 0 1999 | gmx traj -f AA/trajpbc.xtc -s AA/topol.tpr -oxt traj_cg.xtc -n mapping.ndx -com -ng 2000 -b 20000

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1 week 20 hours ago #7923 by molashahimaryam
molashahimaryam replied the topic: multiscaling
How is it possible to make CG pdb file or coarse graining atomistic structure?
Please answer.

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1 week 20 hours ago #7924 by molashahimaryam
molashahimaryam replied the topic: multiscaling
How is it possible to coarse grain atomistic structure ?
please answer
please answer
please answer

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1 week 20 hours 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 week 17 hours ago #7928 by molashahimaryam
molashahimaryam replied the topic: multiscaling
Forever?
Because nobody answers my questions!
What's the target of this forum? banning or helping?

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5 days 37 minutes ago #7932 by molashahimaryam
molashahimaryam replied the topic: multiscaling
Dear Experts
How much should be the size of a simulation box in coarse grained model for a PEO chain consists of 100 monomers?
Thank you

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5 days 34 minutes ago #7933 by molashahimaryam
molashahimaryam replied the topic: multiscaling
Hello
I was banned?

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2 days 16 hours 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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