normal ElNeDyn: Elastic Network in Dynamics

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12 years 9 months ago - 12 years 9 months ago #736 by Kargar
ElNeDyn: Elastic Network in Dynamics was created by Kargar
Dear All,

I started learning ElNeDyn method from tutorial part. There is a pdf file "Howto-ElNeDyn.pdf" in unpacked ElNeDyn-2.1.tar.gz. inside it says:
All the files necessary can be found in:
~periole/FILES_CG2.1/Version_2.1+ElNeDyn
I searched the address " md.chem.rug.nl/~periole/FILES_CG2.1/Version_2.1 " but the page not found. Some files like "protein.itp", written in "Howto-ElNeDyn.pdf", are not in ElNeDyn-2.1.tar.gz file. It would be better if I had them.
By the way I started simulation without any errors, but I am not sour if it is true or not.I am worried about the files .itp I mentioned above. After simulation I expected the shape of protein without changing (I used my protein not the one mentioned in site)
Please help me
Regards
Kargar

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12 years 8 months ago #743 by xavier
Replied by xavier on topic ElNeDyn: Elastic Network in Dynamics
Dear Kargar,

If the file protein.itp is not found is because you are supposed to build it during the tutorial. If you were able to start a simulation this is a good sign :))

Then of course you should check that the different steps you followed finished successfully ... one typical check you should make is the deformation of your protein. I am not sure from your message if you are satisfied or not by your simulation.

XAvier.

Kargar wrote: Dear All,

I started learning ElNeDyn method from tutorial part. There is a pdf file "Howto-ElNeDyn.pdf" in unpacked ElNeDyn-2.1.tar.gz. inside it says:
All the files necessary can be found in:
~periole/FILES_CG2.1/Version_2.1+ElNeDyn
I searched the address " md.chem.rug.nl/~periole/FILES_CG2.1/Version_2.1 " but the page not found. Some files like "protein.itp", written in "Howto-ElNeDyn.pdf", are not in ElNeDyn-2.1.tar.gz file. It would be better if I had them.
By the way I started simulation without any errors, but I am not sour if it is true or not.I am worried about the files .itp I mentioned above. After simulation I expected the shape of protein without changing (I used my protein not the one mentioned in site)
Please help me
Regards
Kargar

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12 years 8 months ago #747 by Kargar
Replied by Kargar on topic ElNeDyn: Elastic Network in Dynamics
Dear XAvier

Thank you for your attention. I have a small (16 amino asides: EAK16-IV) peptide. In atomistic simulation, it is seen that because of electrostatic interactions the peptide bends and form like "U". When I do coarse-graining with MARTINI model, my peptide deforms completely; since in MARTINI model electrostatic potential is screened and not very important. But the shape of peptide is very important for me.
I examined simple elastic model. To keep the shape of peptide I need more than 20 constraints!!! It dose not seem true for a small peptide. So I used ElNeDyn method, then again the peptide deforms completely.
What do you think now? Did I do the simulation well? Do you have any suggestions for this problem?
Thank you in advance
Kargar

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12 years 8 months ago #750 by xavier
Replied by xavier on topic ElNeDyn: Elastic Network in Dynamics
Dear Kargar,

It is not reasonable to think that the peptide can completely deform using ElNeDyn. This method is meant to preserve the conformation of the protein/peptide, while keeping its internal dynamics.

You should check the topology of your peptide and look for the extra bonds that are added by ElNeDyn. Or may be check the deformation it might actually be reasonable!

XAvier.

Kargar wrote: Dear XAvier

Thank you for your attention. I have a small (16 amino asides: EAK16-IV) peptide. In atomistic simulation, it is seen that because of electrostatic interactions the peptide bends and form like "U". When I do coarse-graining with MARTINI model, my peptide deforms completely; since in MARTINI model electrostatic potential is screened and not very important. But the shape of peptide is very important for me.
I examined simple elastic model. To keep the shape of peptide I need more than 20 constraints!!! It dose not seem true for a small peptide. So I used ElNeDyn method, then again the peptide deforms completely.
What do you think now? Did I do the simulation well? Do you have any suggestions for this problem?
Thank you in advance
Kargar

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