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how to add 0.5 M NaCl solution
- cm
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5 years 4 months ago #7948
by cm
how to add 0.5 M NaCl solution was created by cm
hello
i am following this tutorial www.cgmartini.nl/index.php/tutorials-gen...oduction/proteins.My protein has +8 charge.By replacing 8 water molecule by 8 chloride ion,neutralisation is possible.But now i want to add 0.5 M NaCl.How i will do this.
thanking you
i am following this tutorial www.cgmartini.nl/index.php/tutorials-gen...oduction/proteins.My protein has +8 charge.By replacing 8 water molecule by 8 chloride ion,neutralisation is possible.But now i want to add 0.5 M NaCl.How i will do this.
thanking you
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- peterkroon
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5 years 4 months ago #7950
by peterkroon
Replied by peterkroon on topic how to add 0.5 M NaCl solution
It's fairly simple.
0.5M = 0.5 mol/litre (up to you whether that's 0.5 mol Na+ and 0.5 mol of Cl-, or 0.5 mol of NaCl; the latter is more common).
Calculate the volume of your box.
Multiply your volume with 0.5 mol/L, mind the units!
1 mol = 6.022*10^23. Multiply your answer by this.
That should give you the number of ions you need to put into your box, so round it to the nearest integer. The final step is to add those to your .top file, and subtract that number from your number of W particles.
Let's say you start with the following top file and you need to add 150 ions:
Then becomes
Better still, you add WF particles (antifreeze) to make it:
Note that the total number of particle sin your box does not change. Better still, you don't have to change your .gro file (but grompp will give a warning because the names don't match any more).
Good luck!
0.5M = 0.5 mol/litre (up to you whether that's 0.5 mol Na+ and 0.5 mol of Cl-, or 0.5 mol of NaCl; the latter is more common).
Calculate the volume of your box.
Multiply your volume with 0.5 mol/L, mind the units!
1 mol = 6.022*10^23. Multiply your answer by this.
That should give you the number of ions you need to put into your box, so round it to the nearest integer. The final step is to add those to your .top file, and subtract that number from your number of W particles.
Let's say you start with the following top file and you need to add 150 ions:
Protein 1
W 1000Then becomes
Protein 1
W 850
NA 75
CL 75Better still, you add WF particles (antifreeze) to make it:
Protein 1
W 765
W 85
NA 75
CL 75Note that the total number of particle sin your box does not change. Better still, you don't have to change your .gro file (but grompp will give a warning because the names don't match any more).
Good luck!
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5 years 4 months ago #7951
by cm
Replied by cm on topic how to add 0.5 M NaCl solution
thank you so much for your reply.
for martini cg system is it possible to add different type of salt like NaCl,NaBr,NaF,NaI with different concentration.Because i want to see the effect of different salts with different concentration.
in the martini_v2.0_ions.itp file it was mentioned that:
note, ions are not to be taken too seriously using a CG presentation.
; long range electrostatic interactions are absent, and for small ions
; the first hydration shell is considered an implicit part of the CG ion.
for martini cg system is it possible to add different type of salt like NaCl,NaBr,NaF,NaI with different concentration.Because i want to see the effect of different salts with different concentration.
in the martini_v2.0_ions.itp file it was mentioned that:
note, ions are not to be taken too seriously using a CG presentation.
; long range electrostatic interactions are absent, and for small ions
; the first hydration shell is considered an implicit part of the CG ion.
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- peterkroon
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5 years 4 months ago #7952
by peterkroon
Replied by peterkroon on topic how to add 0.5 M NaCl solution
Correct. Electrostatics in Martini are at most approximately correct. Please look at some literature to see whether what you're trying to do is possible with the forcefield (well, it's possible, but whether it makes sense/gives physically meaningful results is another). And I don't know if there are parameters for Br- F- and I- available.
I do expect problems, because NaF should be fairly closely bound together in water, if I recall correctly. Due to the implicit hydration shell the separate ions are probably too large for this to happen.
Also note, that divalent ions should be treated with care as well, mostly for the same reasons. See literature.
I do expect problems, because NaF should be fairly closely bound together in water, if I recall correctly. Due to the implicit hydration shell the separate ions are probably too large for this to happen.
Also note, that divalent ions should be treated with care as well, mostly for the same reasons. See literature.
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5 years 4 months ago #7953
by cm
Replied by cm on topic how to add 0.5 M NaCl solution
thank you very much.
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5 years 4 months ago #7954
by tsjerk
Replied by tsjerk on topic how to add 0.5 M NaCl solution
In this limit of smallness, should one still count the volume taken by the protein as solvent? Isn't molality a better approach? Say 0.5M is 1 NaCl per 110 H2O, 1W = 4H2O, which means I need 4*9 = 36 NA and 36 CL. That's a difference that's not to be neglected, so whichever choice needs to be well argumented. My argument is that we simulate a protein in a solution and assume infinite dilution, so it's the ratio with the solvent that counts and not the box volume.
By the way, insane does just this with the -salt 0.5 option
By the way, insane does just this with the -salt 0.5 option
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