[gmx-users] Relative binding free energy from a neutral to a charged molecule

[hannes.loeffler at stfc.ac.uk]

My suggestion would be to look into
http://scitation.aip.org/content/aip/journal/jcp/139/18/10.1063/1.4826261

BTW, a charged molecule _is_ an ion.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Christopher Neale [chris.neale at alum.utoronto.ca]
Sent: 07 May 2016 06:16
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Relative binding free energy from a neutral to a       charged molecule

Maybe this: http://scitation.aip.org/content/aip/journal/jcp/124/22/10.1063/1.2201698 ?

Can't claim to understand it though. If it were me, I'd pick another project or pick another method.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Stefania Evoli <stefania.evoli at kaust.edu.sa>
Sent: 03 May 2016 08:33:15
To: gmx-users at gromacs.org
Subject: [gmx-users] Relative binding free energy from a neutral to a   charged molecule

Dear Users,

I’m trying to perform relative binding free energy calculations for the transformation from a neutral to a charged molecule. I know reading several articles that this kind of transformations are affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). Screening the letterature I found different corrections for ions but nothing for charged molecules.

Can someone suggest me clear articles about that or help me to understand which kind of corrections should I use?

Thank you in advance for every kind of help.
Stefania

—
Dr. Stefania Evoli
Post-Doctoral Fellow
King Abdullah University of Science and Technology
Catalysis center - Bldg. 3, 4th floor, 4231–WS18
Thuwal, Kingdom of Saudi Arabia
stefania.evoli at kaust.edu.sa



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