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how to add ions
- Justin
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13 years 9 months ago #380
by Justin
how to add ions was created by Justin
Dear all,
In my system, there are 4 net charges. I would like to add some ions to neutralize the system. But I have no idea how to add CG ions and find no instruction for this problem.
From the reply to "SA error", I read this: "First ions - how did You define mapping for ions ? If they are there only for neutralizing system, the easiest would be to remove them for SA ( or changing them for normal water bead - so 3 FG_W molecules more in fg.gro and 3 W in cg.gro file and the same in fg top file ) and then introduce them later with g_ion. "
What is the "g_ion"? Is it a new tool for CG gromacs? Or, is it the "genion" in Gromacs?
Many thanks?
Justin
In my system, there are 4 net charges. I would like to add some ions to neutralize the system. But I have no idea how to add CG ions and find no instruction for this problem.
From the reply to "SA error", I read this: "First ions - how did You define mapping for ions ? If they are there only for neutralizing system, the easiest would be to remove them for SA ( or changing them for normal water bead - so 3 FG_W molecules more in fg.gro and 3 W in cg.gro file and the same in fg top file ) and then introduce them later with g_ion. "
What is the "g_ion"? Is it a new tool for CG gromacs? Or, is it the "genion" in Gromacs?
Many thanks?
Justin
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- jonasori
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7 years 9 months ago #5718
by jonasori
Replied by jonasori on topic how to add ions
Well, this is 6 years and 20 minutes late (according to my screen), but for anyone else in a similar pickle, I'll try to contribute something.
As the quoted text noted, there are two ways of doing this. You can either calculate exactly how many ions you need and add them manually to your .top file (as a new line right under W at the bottom). If you do this, don't forget to subtract the same number from your water beads to keep the total number of residues constant.
Alternatively, one can use genion , which I imagine is what was being referred to with g_ion (or maybe that was just the command that was used 6 years ago). Genion gives you a couple options: most notably, it allows you to just specify a molar concentration (with -conc), rather than a quantity of ions, and have it automatically neutralize itself (-neutral). However, ultimately genion just does what you could do by hand (as described above), and will go into the .top file to switch the residues around. Basically, genion takes a couple more steps but can save you some calculations (i.e. converting molarity to number of ions, based on box-size, etc).
I still use Gromacs 4.X, but I believe that Gromacs 5 has done away with genion and replaced it with gmx_solvate and another. Worth looking into if that's the system you're running.
I doubt this is of any use to Justin, but perhaps others will find it useful. Still, in Justin's case, you could either add 4 negative ions to balance the four positive ones, or have genion do that with genion -s file.tpr -p cg-something.top -o output.gro -neutral.
Best,
Jonas
As the quoted text noted, there are two ways of doing this. You can either calculate exactly how many ions you need and add them manually to your .top file (as a new line right under W at the bottom). If you do this, don't forget to subtract the same number from your water beads to keep the total number of residues constant.
Alternatively, one can use genion , which I imagine is what was being referred to with g_ion (or maybe that was just the command that was used 6 years ago). Genion gives you a couple options: most notably, it allows you to just specify a molar concentration (with -conc), rather than a quantity of ions, and have it automatically neutralize itself (-neutral). However, ultimately genion just does what you could do by hand (as described above), and will go into the .top file to switch the residues around. Basically, genion takes a couple more steps but can save you some calculations (i.e. converting molarity to number of ions, based on box-size, etc).
I still use Gromacs 4.X, but I believe that Gromacs 5 has done away with genion and replaced it with gmx_solvate and another. Worth looking into if that's the system you're running.
I doubt this is of any use to Justin, but perhaps others will find it useful. Still, in Justin's case, you could either add 4 negative ions to balance the four positive ones, or have genion do that with genion -s file.tpr -p cg-something.top -o output.gro -neutral.
Best,
Jonas
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- peterkroon
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7 years 9 months ago #5720
by peterkroon
Replied by peterkroon on topic how to add ions
Note that the first method (just replacing water beads for ions in the .top file) will NOT work with polarizable water.
My personal method of choice is using gmx genion (in gromacs 5), with an appropriate index file; because this does work with polarizable water.
Lastly, it's always the question whether you want to neutralize the system, or add counter-ions for all charged beads. But that depends on what you are simulating.
My personal method of choice is using gmx genion (in gromacs 5), with an appropriate index file; because this does work with polarizable water.
Lastly, it's always the question whether you want to neutralize the system, or add counter-ions for all charged beads. But that depends on what you are simulating.
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- yogi@martini
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3 years 5 months ago #8753
by yogi@martini
Replied by yogi@martini on topic how to add ions
Hello Peterkroon,
I have a small doubt, while using the gmx genion command, usually we replace water molecules with ions, however, each martini water bead has 4 water molecules so, effectively, we are replacing 4 water molecules with 1 ion, so to correct this error do we have to reduce our concentration by factor of 4 to get concentration that we desire for?
For example, to get -conc 0.15, we will actually use 0.0375 instead?
I have a small doubt, while using the gmx genion command, usually we replace water molecules with ions, however, each martini water bead has 4 water molecules so, effectively, we are replacing 4 water molecules with 1 ion, so to correct this error do we have to reduce our concentration by factor of 4 to get concentration that we desire for?
For example, to get -conc 0.15, we will actually use 0.0375 instead?
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- peterkroon
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3 years 5 months ago #8754
by peterkroon
Replied by peterkroon on topic how to add ions
No, because a Martini ion bead also represents some water molecules (2 to 3).
And how would dividing by 4 give you the concentration? You're completely ignoring the rest of the water in your system.
And how would dividing by 4 give you the concentration? You're completely ignoring the rest of the water in your system.
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