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How to set the bond force constant?
- Leliel
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- Visitor
When i use and read the martinize.py , i found that a series of parameters :
#RES# BEADS BONDS ANGLES DIHEDRALS
# BB-SC SC-SC BB-SC-SC SC-SC-SC
"DA": [spl("SNa SNa SP1 SNa"),
[(0.120,5000),(0.220,5000),(0.320,5000),(0.420,5000),(0.520,5000),],
[(10.0, 100),(20.0, 100),(30.0, 100),(40.0, 100),(50.0, 100),(60.0, 100),(70.0, 100),(80.0, 100)],
[(10.0, 100, 10),(20.0, 100, 10),(30.0, 100, 10),(40.0, 100, 10)],
[(50.0, 100)]],
AND i think they're for nucleic acid, but I cant figure out what's the meaning of 0.120,0.220...?
can you explain each number in one [] for me? i know that 5000/100 are the force constant.
BTW, i had read the paper of MARTINI for protein, but i can't find how you set the force constant. you said the bonded sections (length,angle,dihedral angles,)are obtained by the distribution of the PDB, but I dont know how to get the force constant.
Thanks in advance!
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- jaakko
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I've answered this before here . In short, the script has dummy parameters to test that the script works for DNA but those should not be used for anything, they're just placeholders. (The script does state this if you try to run it with DNA input.) We are working on those DNA parameters and once they're done they'll be added to the website and a new version of the script.
As to your other question, the force constants come from fitting the widths of those distributions.
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- xavier
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- Posts: 416
These numbers are the reference distance for the bonds, the distance you want the bond to fluctuate aroundLeliel wrote: HI,i am undergraduate student, learning Martini FF.
When i use and read the martinize.py , i found that a series of parameters :
#RES# BEADS BONDS ANGLES DIHEDRALS
# BB-SC SC-SC BB-SC-SC SC-SC-SC
"DA": [spl("SNa SNa SP1 SNa"),
[(0.120,5000),(0.220,5000),(0.320,5000),(0.420,5000),(0.520,5000),],
[(10.0, 100),(20.0, 100),(30.0, 100),(40.0, 100),(50.0, 100),(60.0, 100),(70.0, 100),(80.0, 100)],
[(10.0, 100, 10),(20.0, 100, 10),(30.0, 100, 10),(40.0, 100, 10)],
[(50.0, 100)]],
AND i think they're for nucleic acid, but I cant figure out what's the meaning of 0.120,0.220...?
The numbers are listed for all the bonds defined in the bond section.can you explain each number in one [] for me? i know that 5000/100 are the force constant.
The procedure goes like this:BTW, i had read the paper of MARTINI for protein, but i can't find how you set the force constant. you said the bonded sections (length,angle,dihedral angles,)are obtained by the distribution of the PDB, but I dont know how to get the force constant.
1- you extract the distribution of bond(s) from a source you chose, PDB structures or atomistic simulation, or experimental source.
2- you run a CG simulation with a first topology and you determine the distribution of the same bonds and compare to the "Experimental" ones.
3- you adjust your CG topology to get a better match with the "experimental" distributions. This last step is repeated until you reach the best match possible ... CG topologies are limited in resolution so you won't get all your distributions perfectly.
Thanks in advance!
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- Leliel
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- Visitor
The procedure goes like this:
1- you extract the distribution of bond(s) from a source you chose, PDB structures or atomistic simulation, or experimental source.
2- you run a CG simulation with a first topology and you determine the distribution of the same bonds and compare to the "Experimental" ones.
3- you adjust your CG topology to get a better match with the "experimental" distributions. This last step is repeated until you reach the best match possible ... CG topologies are limited in resolution so you won't get all your distributions perfectly.
So in the first procedure, you mentioned a distribution of bond(s) in atomistic simulation/PDB files, and compared them with the CG simulation ,but i think it's not the best way to adjust the constant: cause the angle A-B-C in Atomistic file cant be exactly the angle beadA-beadB-beadC in coarse grained file. So i think i think it's properly applicable to use a script to transfer the AT files --> CG files in advance and do a statistic work on the CG files.
I'm not sure if i put my point in a clear way ,and do you have the script to transfer a fine grained DNA to a coarse grained one? If you do , it's downloadable in this website just like the martinize.py??
thanks!
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- xavier
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- Posts: 416
I am not sure the DNA is already available in the current script. If so it would be in the martinize.py script. If not you'd have to be patient.
Leliel wrote:
The procedure goes like this:
1- you extract the distribution of bond(s) from a source you chose, PDB structures or atomistic simulation, or experimental source.
2- you run a CG simulation with a first topology and you determine the distribution of the same bonds and compare to the "Experimental" ones.
3- you adjust your CG topology to get a better match with the "experimental" distributions. This last step is repeated until you reach the best match possible ... CG topologies are limited in resolution so you won't get all your distributions perfectly.
So in the first procedure, you mentioned a distribution of bond(s) in atomistic simulation/PDB files, and compared them with the CG simulation ,but i think it's not the best way to adjust the constant: cause the angle A-B-C in Atomistic file cant be exactly the angle beadA-beadB-beadC in coarse grained file. So i think i think it's properly applicable to use a script to transfer the AT files --> CG files in advance and do a statistic work on the CG files.
I'm not sure if i put my point in a clear way ,and do you have the script to transfer a fine grained DNA to a coarse grained one? If you do , it's downloadable in this website just like the martinize.py??
thanks!
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- xavier
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- Posts: 416
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- yogi@martini
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