normal Protein structure collapsing

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3 months 1 day ago #9725 by aabhatt
Protein structure collapsing was created by aabhatt
Hi,

I want to simulate a protein with a membrane using Martini 3.0 + elastic approach, and I am following the tutorial at www.cgmartini.nl/index.php/tutorials/37-...11-tutorial-proteins .

martinize2  -f step3_input.gro -o protein_martini.top -x fittedprotein_proa.cg.pdb -dssp
~/anaconda3/bin/mkdssp -p backbone -ff martini3001 -elastic -ef 3000 -el 0.5.

Even when I apply a force of 8000, my structure collapses after 10-20 ns (in its 3D configuration).
Could you please provide any suggestions regarding the problem?


Regards,

Aashish

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3 months 1 day ago #9726 by bart
Replied by bart on topic Protein structure collapsing
Did you try doing the tutorial with the default protein first? Then we can be sure everything is working fine for you.

Also, a higher force constant is not equal to higher stability.

Given the information you have provided there is little more I can do for you atm.

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3 months 16 hours ago #9727 by aabhatt
Replied by aabhatt on topic Protein structure collapsing
No i have not try default protein.

okay i will check again.

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2 months 4 weeks ago #9728 by aabhatt
Replied by aabhatt on topic Protein structure collapsing
Hi,

I have checked with the Martini 2.2 (1000 force) and it's perfectly fine.

In Martini 3.0, I increased the upper cutoff from 0.9 to 1.2, and the protein pore is not completely collapsing; it is partially collapsing.

Could you provide an idea about the upper and lower cutoff values? What do they actually mean? Are the lower and upper cutoff values regarding the z-coordinate of the protein or something else?

Regards,

Aashish

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