Dear community, Thanks for your kind answer, Berk! I am actually trying to understand the "RF-excl" term, which comes from one of your contributions to version 3.3.:
http://www.gromacs.org/content/view/18/132/ If you will, I have a couple of perhaps naive questions: 1) 2 sentences appear to be in contradiction, to me: a) The sentence "The 1-4 energies are now reported without reaction-field correction.", that I cite from the web page above, describing the RF-excl feature, and b) "The reaction-field correction should also be applied to all excluded atoms pairs, including self pairs, in which case the normal Coulomb term in eqns. 4.12 and 4.16 is absent.", that I cite from the manual of version 3.3, page 45. If I understand well, ecluded atom interaction pairs are selfinteracting atoms or 1-4 interacting atoms. These sentences would mean that the reaction field correction is applied to the former but NOT to the latter? 2) I don't exactly understand the "self pair" of the sentence I cite in 1 a). To compute a self pair interaction, we would obtain i=j in rij of equations 4.12 and equation 4.16 of the same manual page, making Vcrf and Fi equal to zero. How could one then apply any reaction-field correction, as suggested in the sentence cited in 1 a)? 3) Is the RF-excl term equal to the reaction field correction "Krf*Rij^2 - Crf" of eq. 4.13., or to the constant Crf (eq 4.15.)? I thank you very much for any info! Regards, Pascal ******************************************************************************* Pascal Baillod (PhD student) ******************************************************************************* Swiss Federal Institute of Technology EPFL Tel: +41-(0)21-693-0322 Institute of Chemical Sciences and Engineering , Fax: +41-(0)21-693-0320 Laboratory of Computational Chemistry and Biochemistry [EMAIL PROTECTED] Room BCH 4121, Avenue Forel, http://lcbcpc21.epfl.ch CH-1015 Lausanne ******************************************************************************* _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
