## Re: [apbs-users] Fwd: electric field

 Re: [apbs-users] Fwd: electric field From: Baker, Nathan - 2014-03-15 21:21:55 Attachments: Message as HTML ```Thanks, Andrew! -- Nathan Baker Laboratory Fellow and Technical Group Manager Applied Statistics and Computational Modeling Pacific Northwest National Laboratory +1-509-375-3997 http://www.linkedin.com/in/nathanandrewbaker/ From: Andrew Ritchie [mailto:drew.w.ritchie@...] Sent: Friday, March 14, 2014 10:21 To: apbs-users@... Cc: apbs-users@... Subject: Re: [apbs-users] Fwd: electric field Greetings Neha, These are the sorts of calculations my group spends a lot of time on. To computer the electric field at a point we insert dummy atoms with zero charge around the point of interest and, using the "write atompot flat" keyword, apbs calculates the potential at each atom. We then take the negative potential gradient along each vector we have dummy atoms. ie: ^ y | ---> x Dy1 Dx1 X Dx2 Dy2 Where DZN is dummy atom N along vector Z. The Ey = - (potential_Dy2 - potential_Dy1)/(position_Dy2 - position_Dy1) and Ex = - (potential_Dx2 - potential_Dx1)(position_Dx2 - position_Dx1). Clearly this is trivially expanded into 3 dimensions. We also now use the analytic coulomb potential plus the numeric reaction field potential, as suggested by Dr. Baker per the discussion here: http://sourceforge.net/p/apbs/mailman/message/30808940/ I hope this helps. All the best, Andrew Ritchie On Friday, March 14, 2014 6:03:10 AM UTC-5, Neha Gandhi wrote: Dear List, I was looking for previous mailing list but I didn't get a straight forward answer. Can I use apbs to calculate the electric field vector at a single site at every snapshot of an MD trajectory e.g. electric field dependency of amide proton of glycine on the basis of the electrical field induced by a phosphate group in a protein? My apologies for ignorance Many thanks, Neha -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate ```

 [apbs-users] Fwd: electric field From: Neha Gandhi - 2014-03-14 11:03:17 Attachments: Message as HTML ```Dear List, I was looking for previous mailing list but I didn't get a straight forward answer. Can I use apbs to calculate the electric field vector* at a single site at every snapshot of an MD ** trajectory e.g. electric field dependency of *amide proton of glycine on the basis of the electrical field induced by a phosphate group in a protein? My apologies for ignorance Many thanks, Neha -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate ```
 Re: [apbs-users] Fwd: electric field From: Baker, Nathan - 2014-03-15 21:21:55 Attachments: Message as HTML ```Thanks, Andrew! -- Nathan Baker Laboratory Fellow and Technical Group Manager Applied Statistics and Computational Modeling Pacific Northwest National Laboratory +1-509-375-3997 http://www.linkedin.com/in/nathanandrewbaker/ From: Andrew Ritchie [mailto:drew.w.ritchie@...] Sent: Friday, March 14, 2014 10:21 To: apbs-users@... Cc: apbs-users@... Subject: Re: [apbs-users] Fwd: electric field Greetings Neha, These are the sorts of calculations my group spends a lot of time on. To computer the electric field at a point we insert dummy atoms with zero charge around the point of interest and, using the "write atompot flat" keyword, apbs calculates the potential at each atom. We then take the negative potential gradient along each vector we have dummy atoms. ie: ^ y | ---> x Dy1 Dx1 X Dx2 Dy2 Where DZN is dummy atom N along vector Z. The Ey = - (potential_Dy2 - potential_Dy1)/(position_Dy2 - position_Dy1) and Ex = - (potential_Dx2 - potential_Dx1)(position_Dx2 - position_Dx1). Clearly this is trivially expanded into 3 dimensions. We also now use the analytic coulomb potential plus the numeric reaction field potential, as suggested by Dr. Baker per the discussion here: http://sourceforge.net/p/apbs/mailman/message/30808940/ I hope this helps. All the best, Andrew Ritchie On Friday, March 14, 2014 6:03:10 AM UTC-5, Neha Gandhi wrote: Dear List, I was looking for previous mailing list but I didn't get a straight forward answer. Can I use apbs to calculate the electric field vector at a single site at every snapshot of an MD trajectory e.g. electric field dependency of amide proton of glycine on the basis of the electrical field induced by a phosphate group in a protein? My apologies for ignorance Many thanks, Neha -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate ```