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-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Christopher Neale [chris.ne...@alum.utoronto.ca] Sent: 07 May 2016 06:16 To: gmx-us...@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-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Stefania Evoli <stefania.ev...@kaust.edu.sa> Sent: 03 May 2016 08:33:15 To: gmx-us...@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.ev...@kaust.edu.sa ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
