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Elnedyn
- anuvc84
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10 years 9 months ago #1776
by anuvc84
Elnedyn was created by anuvc84
Dear users,
I tried CG simulation using elnedyn FF (Rc=0.9; KSpring=500KJ/mol/nm2) with protein in water (octamer in the form of a helical filament). During the simulation, the helical filaments got circularised.
I would like to know whether there is any way by which the helicity of the filaments can be maintained (restrained) during simulation.
Thanking You,
regards,
Anu
I tried CG simulation using elnedyn FF (Rc=0.9; KSpring=500KJ/mol/nm2) with protein in water (octamer in the form of a helical filament). During the simulation, the helical filaments got circularised.
I would like to know whether there is any way by which the helicity of the filaments can be maintained (restrained) during simulation.
Thanking You,
regards,
Anu
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- xavier
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10 years 9 months ago #1777
by xavier
Replied by xavier on topic Elnedyn
Hi Anu,
It is not clear what the circularization of the filament means! I can guess that it is a significant conformational change that you are happy about. Could you try to describe it in more detail.
Did you build an EN for each subunit? Would it make sense to use a global EN in this particular case?
It is not clear what the circularization of the filament means! I can guess that it is a significant conformational change that you are happy about. Could you try to describe it in more detail.
Did you build an EN for each subunit? Would it make sense to use a global EN in this particular case?
anuvc84 wrote: Dear users,
I tried CG simulation using elnedyn FF (Rc=0.9; KSpring=500KJ/mol/nm2) with protein in water (octamer in the form of a helical filament). During the simulation, the helical filaments got circularised.
I would like to know whether there is any way by which the helicity of the filaments can be maintained (restrained) during simulation.
Thanking You,
regards,
Anu
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- anuvc84
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10 years 9 months ago #1782
by anuvc84
Replied by anuvc84 on topic Elnedyn
the protein i tried to simulate is an octamer modelled in the form of a helix ( one turn of a helix is formed by 6 monomers). We were looking for the changes in the helical filament rather than a complete collapse of helix ( decrease of the pitch drastically as the model cicularise).So if there is a way to put restraints, the helical nature of the filament could be maintained.I tried simulation with martini22 forcefield before.Then also during the simulation the helical filament got circularised.
Now I used the martinize.py script with -ff elnedyn and Rc and Kspring values, 0.9 and 500 respectively to generate the CG model and topology for the octamer.
regards
Anu
Now I used the martinize.py script with -ff elnedyn and Rc and Kspring values, 0.9 and 500 respectively to generate the CG model and topology for the octamer.
regards
Anu
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- anuvc84
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10 years 9 months ago #1793
by anuvc84
Replied by anuvc84 on topic Elnedyn
Dear users,
I would like to know what is the maximum value of Rc and Kspring we can use with ElNeDyn FF.
Sorry for my ignorance, how will we build EN scaffold for each domain separately?
Thanking You,
regards
Anu
I would like to know what is the maximum value of Rc and Kspring we can use with ElNeDyn FF.
Sorry for my ignorance, how will we build EN scaffold for each domain separately?
Thanking You,
regards
Anu
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- xavier
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10 years 9 months ago #1794
by xavier
Replied by xavier on topic Elnedyn
The values you use are standard and guaranty a reasonable behaviour of your protein. For refinement you'd need to run some atomistic simulation and look at matching the RMSF per residue. It is also important to check that large amplitude motion are well described. This is possible by running a PCA on the atomistic coordinate along the trajectory.
This is described in the original paper (Periole et al, JCTC-2009)
In other words there is no magic maximum value for Rc and Kspring but I would not go larger than 1.0/1000.
The definition of separate EN for protein domains is not supported by martinize but you can play with the options to do it, one by one.
This is described in the original paper (Periole et al, JCTC-2009)
In other words there is no magic maximum value for Rc and Kspring but I would not go larger than 1.0/1000.
The definition of separate EN for protein domains is not supported by martinize but you can play with the options to do it, one by one.
anuvc84 wrote: Dear users,
I would like to know what is the maximum value of Rc and Kspring we can use with ElNeDyn FF.
Sorry for my ignorance, how will we build EN scaffold for each domain separately?
Thanking You,
regards
Anu
Please Log in or Create an account to join the conversation.
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