Gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral

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1

GROMACS version: gmx genion, version 2020.1-Ubuntu-2020.1-1
GROMACS modification: Yes/No
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I have problem when I run this command, there is no the serial number of solution 15 , how can I solve this ?

2

Hi,
gmx genion needs as input an index file with the water molecules. This is missing in your case. You can check if your tpr file contains information on water molecules.
\Alessandra

3

Mam, I am also facing the same problem.
Can you tell me how to check ions.tpr file?

4

Hi @alevilla @jalemkul @hess

Curious to know how genion calculates the number of ions to be added into the system. Does it calculate based on the number of water molecules present in the system or there is some another method?

I have found some explanation as below (https://www.r-ccs.riken.jp/labs/cbrt/tutorials2022/tutorial-2-3/):

Now, remember basic chemistry. Since we specified 150 mM NaCl solution, the number of moles of solute in 1 litter (L) solution should be 150 mmol. The Avogadro number is 6.02 × 1023. Accordingly, there are 150 × 10-3 × 6.02 × 1023 = 9.03 × 1022 NaCl molecules in the 1 L NaCl solution. Here, we assume that the density of NaCl solution is almost same with that of solvent. The density of water is ~0.997 g/cm3 at the room temperature, and thus, the weight of 1 L water is ~997 g. Since the weight of 1 mol H2O is ~18.02 g, the 1 L water is composed of ~3.33 × 1025 H2O molecules (55.3 mol). According to these relationships, when there are *N* water molecules in the system, we should add (9.03 × 1022)/(3.33 ×1025) × *N* = **0.002712 × *N*** NaCl molecules in the system to make 150 mM NaCl solution. In the case of *N* = 7,882, this equation gives ~21.4, which is close to the number of Cl− in the constructed system. Actually, 4 more Na+ were added to the system than Cl−. This is because Protein G has a total net charge of −4, and the corresponding positive charge was needed to neutralize the system, which is required to use the particle mesh Ewald method (PME) in the MD simulations.

Is it same as above or different? Because the calculation for the number of ions to be added into system, is different from the actually added ions by genion.

Please consider it.

5

Hi,
Sorry, do you refer to the command line in the title?

gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral

Then enough ions are added to neutralize the system.
Otherwise to which combination of options do you refer to?
\Alessandra

6

genion simply computes the volume of the box and then calculates the number of each species to be added to reach the specified concentration in mol/L. It does not take into account excluded volume of solute molecules, which may or may not be a significant deviation from what should be done.

if (conc > 0)
{
    /* Compute number of ions to be added */
    vol   = det(box);
    nsalt = gmx::roundToInt(conc * vol * gmx::c_avogadro / 1e24);
    p_num = abs(nsalt * n_q);
    n_num = abs(nsalt * p_q);
}
7

Hi,

yes I use the command

gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.15

so query is how does the genion calculates the number of ions to neutralize the system, based on the provided concentration and the box size (in the previous step).
Thanks…

8

Hi,
Thank for your time.

so does that mean, the added ions are independent of the numbers of size of protein/Ligand and the number of the water molecules added.

Could you please explain the below equation (Lets say conc = 0.15 and box size= 10 A cubic)

Thanks