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normal Difference between solvate in MARTINI and GROMACS?

  • darrenphua
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3 years 9 months ago #8639 by darrenphua
Difference between solvate in MARTINI and GROMACS? was created 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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3 years 9 months ago #8640 by riccardo
Replied by riccardo on topic Difference between solvate in MARTINI and GROMACS?
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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3 years 9 months ago #8641 by darrenphua
Replied by darrenphua on topic Difference between solvate in MARTINI and GROMACS?
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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3 years 9 months ago #8642 by darrenphua
Replied by darrenphua on topic Difference between solvate in MARTINI and GROMACS?
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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