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MARTINI for cyclodextrins
- darrenphua
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3 years 9 months ago #8633
by darrenphua
MARTINI for cyclodextrins was created by darrenphua
I'm having difficulty understanding how to use martini for visualization of coarse grained models with VMD or other visualization software.
First, can martini models be visualized only in VMD?
What are the exact steps required?
I have tried reading through the VMD manual and i have the cyclodextrins .itp and .gro files downloaded, but I need help with the exact steps to take.
I suppose there is something to do with scripting?
Next question i have: how will martini define the connecting particles? Is there a file that i need to download to define this or will it be done automatically in a modeling software?
And my final question: if i were to run martini models in GROMACS, will there be any difference in the workflow from running typical simulations?
I am familiar with adding new molecules to topology file and including the relevant .itp files for molecules that i parameterize on servers such as SwissParam.
Will Martini be much different from this?
Thanks a lot in advance for anyone who can help me with these!
First, can martini models be visualized only in VMD?
What are the exact steps required?
I have tried reading through the VMD manual and i have the cyclodextrins .itp and .gro files downloaded, but I need help with the exact steps to take.
I suppose there is something to do with scripting?
Next question i have: how will martini define the connecting particles? Is there a file that i need to download to define this or will it be done automatically in a modeling software?
And my final question: if i were to run martini models in GROMACS, will there be any difference in the workflow from running typical simulations?
I am familiar with adding new molecules to topology file and including the relevant .itp files for molecules that i parameterize on servers such as SwissParam.
Will Martini be much different from this?
Thanks a lot in advance for anyone who can help me with these!
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- bart
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3 years 9 months ago - 3 years 9 months ago #8634
by bart
Replied by bart on topic MARTINI for cyclodextrins
Dear Martini User,
1) martini is just a point cloud trajectory like any other MD trajectory or lardar/radar trajectory. Even tomography data shares many features. Therefore all visualization software for such data types could work for Martini. However, it is not always the case that the default MD file formats are supported. VMD works well if you use cg_bonds (there is a visualization tutorial on this webpage) or a bond annotated file format for trajectories (newer gromacs format). For basic visualization UnityMol can do wonders with out of the box Martini support (protein, DNA, lipid recognition), but isn't as feature rich ad VMD.
2) the basic workflow is identical for CG vs AA. Some relevant other things are: CG works well with NPT, NVE is usually questioned (though this is an oncoming discussion). Numerical equilibration for a CG system is quite trivial compared to AA due to the softer potentials.
In short, read the cg_bonds tutorial and don't treat your rough CG systems with the silk gloves for atomistic systems (it's just not needed in many cases). Do the lipids tutorial and you will see what I mean.
Cheers,
Bart
1) martini is just a point cloud trajectory like any other MD trajectory or lardar/radar trajectory. Even tomography data shares many features. Therefore all visualization software for such data types could work for Martini. However, it is not always the case that the default MD file formats are supported. VMD works well if you use cg_bonds (there is a visualization tutorial on this webpage) or a bond annotated file format for trajectories (newer gromacs format). For basic visualization UnityMol can do wonders with out of the box Martini support (protein, DNA, lipid recognition), but isn't as feature rich ad VMD.
2) the basic workflow is identical for CG vs AA. Some relevant other things are: CG works well with NPT, NVE is usually questioned (though this is an oncoming discussion). Numerical equilibration for a CG system is quite trivial compared to AA due to the softer potentials.
In short, read the cg_bonds tutorial and don't treat your rough CG systems with the silk gloves for atomistic systems (it's just not needed in many cases). Do the lipids tutorial and you will see what I mean.
Cheers,
Bart
Last edit: 3 years 9 months ago by bart.
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- darrenphua
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3 years 9 months ago #8635
by darrenphua
Replied by darrenphua on topic MARTINI for cyclodextrins
Hi Bart,
Thanks for your reply!
I realised that VMD is meant to work with UNIX but i'm currently running it on windows.
The command line language is very different for windows and i don't understand how to convert the instructions into the type that is recognised on windows.
I'm stuck at the first step which is to source for the cg_bonds-v5.tcl file.
Thanks for your reply!
I realised that VMD is meant to work with UNIX but i'm currently running it on windows.
The command line language is very different for windows and i don't understand how to convert the instructions into the type that is recognised on windows.
I'm stuck at the first step which is to source for the cg_bonds-v5.tcl file.
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