Hi Jason,
Thanks for that...
addIonsRand works fine, both neutralizing the model and adding additional ions/salt. All ions are positions within the water box even at smaller sized boxes (such as 10A) which caused the "No solvent overlap" problem in the electrostatic positioning of ions (i.e. addions).
Cheers
Johannes
>Date: Mon, 6 May 2013 23:19:25 -0400
>From: Jason Swails <jason.swails.gmail.com<mailto:jason.swails.gmail.com>>
>Subject: Re: [AMBER] Leap adding salt No solvent overlap
>To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
>
>Try using "addIonsRand" instead of "addIons". Does that work? (Note, it
>adds ions in random positions rather than according to electrostatic
>potential).
>HTH,
>Jason
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 07 2013 - 17:00:03 PDT
