[gmx-users] genion problem with divalent ions

2012-09-09 Thread Matthias Ernst
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

Re: [gmx-users] genion problem with divalent ions

2012-09-09 Thread Justin Lemkul
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

Re: [gmx-users] genion problem with divalent ions

2012-09-09 Thread Leandro Bortot
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.