I know how to change the ionic concentration by -conc command but, what is the default ion concentration that gets set while adding ions for neutralization in gromacs?
There isn't one. The -neutral flag adds whatever ions are necessary to neutralize the system. That number is system-dependent, so there is no default, and these ions generally aren't really thought of as part of any actual salt concentration.
There isn't one. The -neutral flag adds whatever ions are necessary to neutralize the system. That number is system-dependent, so there is no default, and these ions generally aren't really thought of as part of any actual salt concentration.
What about adding ions in the system?
How should I know, what is the number of charges that needs to be added?
I have read through the tutorial, it mentioned that we need to refer the last line of [atoms] directive in topol.top. But, mine was -7. Should it be fine to add on negative value of charges into the system?
Thanks.
grompp tells you the net charge of the entire system when you create the .tpr file for genion. If your system is already negative, you definitely should not add more negative charges...
Ok Justin, thanks! So, when my total charge system was in negative charge (-7), I should add the positive ion into the system. Right?
Thus, the command should be,
gmx genion -s ions.tpr -o 1F0P_solv_ions.gro -p topol.top -pname NA -nname CL -np 7
Please correct me if I'm wrong.
Thanks.
Well -7 + 7 = 0 so it's clearly neutral.
Whether or not that is the best way to simulate the system is another matter. You need to determine if ionic strength (e.g. physiological, or some other condition) is what you should be modeling, how well the force field's ion parameters represent such solutions, etc.
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