normal Difference between solvate in MARTINI and GROMACS?

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4 weeks 1 day ago #8639 by darrenphua
What is the purpose of having the initial water box water.gro for gmx solvate with when dealing with martini models?

Why not the usual process of gmx solvate without the input .gro file as with typical gromacs?

For martini, it looks like a water box is already defined and then combined with the protein during gmx solvate, instead of adding water to fill the box directly?

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4 weeks 1 day ago #8640 by riccardo
The gromacs tool 'gmx solvate' by default solvates with *atomistic* water. But it can potentially use as solvent anything else (e.g., an atomistic solvent different from water, or a CG solvent), *provided that* you pass to the tool a box with the solvent you want (using the flab "-cs"). This should answer your question. See also "gmx help solvate".

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4 weeks 1 day ago #8641 by darrenphua
If i understand correctly, the default gmx solvate will use the defined box as the size of system to put atomistic water inside. On the other hand, if other solvents or corase grained water is desired, then the user has to supply the box of solvent molecules?
What about providing just 1 solvent molecule as the reference template? Does it work this way too?
And if not, it seems that the solvent box must be larger than the existing system?

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4 weeks 1 day ago #8642 by darrenphua
Sorry i might have been confused slightly! I understand how gmx solvate works now :) found the trend in both gromacs and martini

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