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Single lipid configuration
- prithwish
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7 years 10 months ago #5695
by prithwish
Single lipid configuration was created by prithwish
Hello,
I am new in CG MD field. As a starting point, I followed the tutorial given in Martini webpage.
I am interested in lipid self-assembly. Therefore, to create a starting configuration of a mixture of lipid and water, I need a configuration of the single lipid molecule, i.e. the coordinates of the beads representing the lipid.
I am interested for the lipid, Monoolein (2,3-dihydroxypropyl (Z)-octadec-9-enoate ).
In order to define the beads and the coordinates of a single Monnolein molecule in CG formalism, is there any standard procedure ?
I have another question regarding the 'POSITION RESTRAINT' option in the lipid topology file. I have seen that for a few lipid structures, the position restraint is mentioned in topology (martini_v2.0_lipids.itp). What is the mdp option to enable the 'position restraint' part of the .itp file?
Thanks and kind regards,
-
PKN
I am new in CG MD field. As a starting point, I followed the tutorial given in Martini webpage.
I am interested in lipid self-assembly. Therefore, to create a starting configuration of a mixture of lipid and water, I need a configuration of the single lipid molecule, i.e. the coordinates of the beads representing the lipid.
I am interested for the lipid, Monoolein (2,3-dihydroxypropyl (Z)-octadec-9-enoate ).
In order to define the beads and the coordinates of a single Monnolein molecule in CG formalism, is there any standard procedure ?
I have another question regarding the 'POSITION RESTRAINT' option in the lipid topology file. I have seen that for a few lipid structures, the position restraint is mentioned in topology (martini_v2.0_lipids.itp). What is the mdp option to enable the 'position restraint' part of the .itp file?
Thanks and kind regards,
-
PKN
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- helgi
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7 years 10 months ago #5704
by helgi
Replied by helgi on topic Single lipid configuration
Hello, hello,
The short answer is that it really depends.
If you already have the CG topology and only need an initial coordinate file you can just place the correct number of beads in a box (or roughly at the correct position) and run energy minimization.
If you want to create a new Martini lipid CG topology you will have to run atomistic reference simulations of the lipids under different conditions, gather available experimental data and iteratively improve your CG model until you got a “satisfactory” agreement. If you want the model to be very good this can be a significantly large project on it’s own.
If you only want a rough CG Model and other CG models for similar lipids exist (e.g. lyso-lipids) you could modify that CG model to your needs, but you would still have to verify that your modifications make sense (e.g. compare to experimentally determined behavior and atomistic simulations).
For your other question there should not be any 'POSITION RESTRAINT' in the “martini_v2.0_lipids.itp” file, you should double check your file. In general in GROMOS a specific 'POSITION RESTRAINT' file can be imported e.g. right after you import your protein topology or in your topology file the 'POSITION RESTRAINT' section can be included normally in a if statement, ‘ifdef XXX’, and you can set XXX by defining it in your .mdp file ‘define = -DXXX’.
Cheers,
- Helgi
The short answer is that it really depends.
If you already have the CG topology and only need an initial coordinate file you can just place the correct number of beads in a box (or roughly at the correct position) and run energy minimization.
If you want to create a new Martini lipid CG topology you will have to run atomistic reference simulations of the lipids under different conditions, gather available experimental data and iteratively improve your CG model until you got a “satisfactory” agreement. If you want the model to be very good this can be a significantly large project on it’s own.
If you only want a rough CG Model and other CG models for similar lipids exist (e.g. lyso-lipids) you could modify that CG model to your needs, but you would still have to verify that your modifications make sense (e.g. compare to experimentally determined behavior and atomistic simulations).
For your other question there should not be any 'POSITION RESTRAINT' in the “martini_v2.0_lipids.itp” file, you should double check your file. In general in GROMOS a specific 'POSITION RESTRAINT' file can be imported e.g. right after you import your protein topology or in your topology file the 'POSITION RESTRAINT' section can be included normally in a if statement, ‘ifdef XXX’, and you can set XXX by defining it in your .mdp file ‘define = -DXXX’.
Cheers,
- Helgi
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