Hi,
I just encountered (another) strange thing with genion.
I wanted to neutralized a system by adding Mg-Ions (charge in ions.itp:
2, forcefield amber99sb), so I expected half of the system charge (-52)
to be added as ions. BUT it added the same amount, i.e. 52 Mg ions
instead of 26 which
On 9/9/12 7:53 AM, Matthias Ernst wrote:
Hi,
I just encountered (another) strange thing with genion.
I wanted to neutralized a system by adding Mg-Ions (charge in ions.itp: 2,
forcefield amber99sb), so I expected half of the system charge (-52) to be added
as ions. BUT it added the same
Hi there,
In addition to setting -pq to 2 as Justin said, you can set -conc to a
very low value such as 0.1 for neutralizing the system.
One more thing... genion apparently uses the box volume when
determining how many ions are necessary for getting a given ionic strength.
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