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solvent molecules
- nanogod
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5 years 7 months ago #7787
by nanogod
solvent molecules was created by nanogod
Hi,
I have a stupid question that I am sure I should know, but havent done md simulations for some time :)
In the "martini_v2.0_solvents.itp" alot of solvents are represented. however, how do i obtain the CG.gro file for these solvents?
Thanks for the help.
Best regards
Morten
I have a stupid question that I am sure I should know, but havent done md simulations for some time :)
In the "martini_v2.0_solvents.itp" alot of solvents are represented. however, how do i obtain the CG.gro file for these solvents?
Thanks for the help.
Best regards
Morten
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- Pim
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5 years 7 months ago #7788
by Pim
Replied by Pim on topic solvent molecules
Hi,
We don't have all solvent gros available, for some part you have to make them yourselves. Most solvents are 1,2,3 or max 4 beads, to it's usually quite ok to do that. You can get inspiration from the Downloads-->Example applications section, where you can find water (1 bead), hexadecane slab (4 beads), some octane (2 beads, e.g. fullerene in octane). If you rename the beads and remove some other things you can make a solvent box, equilibrate it and use it. Martini simulations are often so forgiving that you can start from a situation with some overlap or holes without it crashing.
Good luck, Pim
We don't have all solvent gros available, for some part you have to make them yourselves. Most solvents are 1,2,3 or max 4 beads, to it's usually quite ok to do that. You can get inspiration from the Downloads-->Example applications section, where you can find water (1 bead), hexadecane slab (4 beads), some octane (2 beads, e.g. fullerene in octane). If you rename the beads and remove some other things you can make a solvent box, equilibrate it and use it. Martini simulations are often so forgiving that you can start from a situation with some overlap or holes without it crashing.
Good luck, Pim
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