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MARTINI simulation of protein-protein assosiation
- Pim
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7 years 10 months ago #5678
by Pim
Replied by Pim on topic MARTINI simulation of protein-protein assosiation
If dissociation would be an option this would be nice, but it sounds like this is not the case so you could save simulation time by stopping the simulations after the complex has associated indeed.
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- James Starlight
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7 years 10 months ago - 7 years 10 months ago #5679
by James Starlight
Replied by James Starlight on topic MARTINI simulation of protein-protein assosiation
The question regarding setups of the simulations of the system parametrized using polarizable force field:
should something be changed within mdp file (I think, mainly cut-offs) for MARTINI simulation for the system parametrized with polarizable force field assuming that I start from mdp file initially used for the no-polarizable of the same system?
For my particular case I start simulation with 0.01 integration time step and everything is fine during equilibration with position restrains applied on protein atoms;
than I switch to production run - increasing integration step to 0.002 and removing restraits after which the system crashed immediately :-)
also I use -rdd 1.4 for those runs which produce better stability for my particular case
should something be changed within mdp file (I think, mainly cut-offs) for MARTINI simulation for the system parametrized with polarizable force field assuming that I start from mdp file initially used for the no-polarizable of the same system?
For my particular case I start simulation with 0.01 integration time step and everything is fine during equilibration with position restrains applied on protein atoms;
than I switch to production run - increasing integration step to 0.002 and removing restraits after which the system crashed immediately :-)
also I use -rdd 1.4 for those runs which produce better stability for my particular case
Last edit: 7 years 10 months ago by James Starlight.
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7 years 10 months ago #5680
by Pim
Replied by Pim on topic MARTINI simulation of protein-protein assosiation
Don't change the cut-offs as stated before. I also don't know why you use a 10 fs time step, 20-30 fs is recommended. I'm also not sure if you mean 0.02 instead of 0.002? 0.02 should be stable with only proteins, lipids and ions in your system. The main/only thing you should change going to polarisable force field is epsilon_r from 15 to 2.5. All details can be found at
cgmartini.nl/images/parameters/exampleMD...ini_v2.x_example.mdp
mdrun -rdd has no effect on the cut-offs of the force field, it's simply gromacs's way to create the bonded charged group neighbour list in parallelized simulation. Sometimes 1.6 is even useful to improve the stability of simulations of highly parallelized systems but especially if you don't get warnings from grompp this should not be a reason for simulations to immediately crash.
mdrun -rdd has no effect on the cut-offs of the force field, it's simply gromacs's way to create the bonded charged group neighbour list in parallelized simulation. Sometimes 1.6 is even useful to improve the stability of simulations of highly parallelized systems but especially if you don't get warnings from grompp this should not be a reason for simulations to immediately crash.
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- James Starlight
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7 years 10 months ago #5686
by James Starlight
Replied by James Starlight on topic MARTINI simulation of protein-protein assosiation
Thanks for the suggestions again!
You are right I use dt= 0.01 for the equilibration stage, and then switching to dt=0.02 in productiom run -> the simulation has been crashed producing alot of lincs warnings! Now I try to reduce epsilon_r and slightly decrease integration step to 0.015 and see how it will affect the stability of the simulation. Should I also modify -rdd flag provided for mdrun compared to the non-polarizable simulation ?
Gleb
You are right I use dt= 0.01 for the equilibration stage, and then switching to dt=0.02 in productiom run -> the simulation has been crashed producing alot of lincs warnings! Now I try to reduce epsilon_r and slightly decrease integration step to 0.015 and see how it will affect the stability of the simulation. Should I also modify -rdd flag provided for mdrun compared to the non-polarizable simulation ?
Gleb
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- James Starlight
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7 years 9 months ago #5729
by James Starlight
Replied by James Starlight on topic MARTINI simulation of protein-protein assosiation
Dear Martini users!
I wonder to ask whether everyone has some experience with the application of aMD for the MARTINI systems? For my particular system discussed here I am looking for some non-equilibrium Md protocol in GROMACS-5 with the possibilities to apply one or two boosts on the system to accelerate some diffusion events within it, assuming that I am modeling protein-protein binding using polarizable-water martini model.
Thanks!
James
I wonder to ask whether everyone has some experience with the application of aMD for the MARTINI systems? For my particular system discussed here I am looking for some non-equilibrium Md protocol in GROMACS-5 with the possibilities to apply one or two boosts on the system to accelerate some diffusion events within it, assuming that I am modeling protein-protein binding using polarizable-water martini model.
Thanks!
James
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7 years 9 months ago #5730
by peterkroon
Replied by peterkroon on topic MARTINI simulation of protein-protein assosiation
What do you mean with aMD? What type of non-equilibrium protocols/boosts did you have in mind?
Umbrella Sampling (and PMFs in general) have been done, as well as TI (not applicable here).
IIRC things like Transition Path/Interface Sampling (group of P. Bolhuis) have also been done (look for Tipsi).
But I still think you want to do DAFT.
Umbrella Sampling (and PMFs in general) have been done, as well as TI (not applicable here).
IIRC things like Transition Path/Interface Sampling (group of P. Bolhuis) have also been done (look for Tipsi).
But I still think you want to do DAFT.
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7 years 9 months ago #5731
by James Starlight
Replied by James Starlight on topic MARTINI simulation of protein-protein assosiation
What I have asked - It's much simpler than umbrella sampling and TI - it's already implemented in amber and NAMD you just specify what boost will be added to the system in mdp file and run md :-)
www.ks.uiuc.edu/Research/namd/2.9/ug/node63.html
however gromacs developers have told me that this protocol is not planned for next GMX revisions :(
www.ks.uiuc.edu/Research/namd/2.9/ug/node63.html
however gromacs developers have told me that this protocol is not planned for next GMX revisions :(
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7 years 9 months ago #5732
by peterkroon
Replied by peterkroon on topic MARTINI simulation of protein-protein assosiation
Ok, I'm not familiar with the topic.
But Martini is not Gromacs specific, so feel free to use NAMD/Amber. I'm fairly sure the forcefield files are available for NAMD at least. Otherwise, translating them should not be overly complicated.
But Martini is not Gromacs specific, so feel free to use NAMD/Amber. I'm fairly sure the forcefield files are available for NAMD at least. Otherwise, translating them should not be overly complicated.
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