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normal Neutralizing martini system

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11 years 1 week ago #1503 by bt12d026
Neutralizing martini system was created by bt12d026
Dear All,
How to neutralize a coarse grained system?

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11 years 1 week ago #1504 by djurre
Replied by djurre on topic Neutralizing martini system
The same way as for a atomistic system: Add ions. This can for example be done using the Gromacs program genion.

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11 years 1 week ago #1505 by bt12d026
Replied by bt12d026 on topic Neutralizing martini system
Thanks djurre for the immediate reply. So, the ions are same in CG and AA systems. If I define ions in my topology file as #include martini_v2.0_ions.itp, is it fine??

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11 years 1 week ago #1506 by djurre
Replied by djurre on topic Neutralizing martini system
Yes that should be fine. Keep in mind that the Martini ions are often considered "partially hydrated": One ion is said to have +/-2 water incorporated. This might have a miniscule effect when defining the concentration.

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11 years 1 week ago #1507 by bt12d026
Replied by bt12d026 on topic Neutralizing martini system
I have defined the conc. of my system as 0.15mMOL of NACL using genion. It has replaced some 550 W with NA+ and CL- ions. So, does it make any anomaly in my system? Or Should I go for simple neutralization without maintaining any Conc.?

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11 years 1 week ago #1508 by djurre
Replied by djurre on topic Neutralizing martini system
The problem with defining the concentration based on the volume (which is what genion does, as far as I know) is that the volume might change due the relaxation or even the addition of the ions itself. So make sure the concentration is still right after some equilibration simulation. (in other words: measure the volume and calculate the actual concentration).

In my opinion it is often better to define the concentration of ions relative the number of water (knowing that there are ±55.3 mols of water in a liter).

I think it will never hurt to add ions to some buffer concentration.

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11 years 1 week ago #1509 by bt12d026
Replied by bt12d026 on topic Neutralizing martini system
Thank you sir for your valuable suggestions. But my CG system is showing some peculiar density around 1117 kg/m3. The physiological density should be around 1000kg/m3. How to maintain it sir? I have used the CG water (given in the protein in water tutorial) and solvated using the command
genbox -cp cg_protein.gro -cs water.gro -o solvate.gro -p protein.top

Thanks for your valuable time & concern

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11 years 1 week ago #1510 by djurre
Replied by djurre on topic Neutralizing martini system
Might it be that the density of you system is off due to the presence of the protein and or ions?

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