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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>The RF correction is NOT applied to 1-4 pairs.<br>It is applied to excluded pairs, independently of it they interact via 1-4 interaction or not.<br>For RF simply all atom pairs in a cut-off sphere need to be corrected.<br>The simplest way of doing this is correcting the non-bonded potential<br>and correcting all pairs that do not interact via the non-bonded potential (excluded pairs).<br><br>For why one has to correct all pairs with an r^2 function, you have to read the literature.<br><br>Berk.<br></div><br><hr id="stopSpelling">> To: gmx-users@gromacs.org<br>> Date: Wed, 12 Mar 2008 16:26:05 +0100<br>> From: pascal.baillod@epfl.ch<br>> Subject: [gmx-users] RE: Coul-14, LJ-14 and RF-excl definitions (2)<br>> <br>> Dear developers,<br>> <br>> I would again like to thank David, Xavier and Berk for their very informative<br>> explanations on RF-excl and 1-4 interactions. I am still a bit confused, though,<br>> with Berk's very last statement on this issue. If I quote it:<br>> <br>> "The reaction field is not applied to pair (1-4) terms. Therefore there are no<br>> issues with fudgeQQ."<br>> <br>> As far as I understood, the reaction field correction IS applied to (1-4) pairs,<br>> but added to the RF-excl term, and not to Coul-14 term. At least this is what I<br>> understood from another explanation from Berk, sent on the mailing list sometime<br>> around September 2007:<br>> <br>> "The reaction-field correction applies to ALL atom pairs that are within the<br>> cut-off distance(or more accurately: atom pairs for which their charge group<br>> centers are within the cutoff distance). So all "noraml non-bonded interaction<br>> pairs, as well as all excluded pairs including self -pairs. The only issue is to<br>> which energy term wich contribution is added. In old Gromacs versions the RF<br>> correction for 1-4 pairs was added to the 1-4 energy term. In the newer version<br>> its added to the RF-excl term."<br>> <br>> <br>> I would also like understand why the reaction field correction is applied to<br>> excluded atom pairs. The corrected coulomb potential described in the manual<br>> reads (please open the attached pdf for the compiled equations):<br>> <br>> V_{crf} = f *q_i *q_j [ \frac{1}{r_{ij}} + k_{rf}r^2_{ij} - c_{rf} ] (1)<br>> <br>> This is equivalent to<br>> <br>> V_{crf} = V_c + V_{rf} (2)<br>> <br>> where V_c is the usual Coulomb potential energy, and V_{rf} is the <br>> reaction field correction.<br>> <br>> For excluded atom pairs, there is no Coulomb interaction, except for 1-4 pairs,<br>> where there is a reduced Coulomb interaction. However, in agreement with what I<br>> state above, the code dose seem to compute a reaction field correction for all<br>> excluded atom pairs. In the RF_excl_correction routine of mdlib/rf_util.c, this<br>> correction reads:<br>> <br>> V_{rf} = f q_i q_j ( k_{rf}r^2_{ij} - c_{rf} )<br>> <br>> That means we apply a potential that is a function of r^2, yielding a force<br>> whose magnitude increses with r and whose direction is opposed to the Coulomb<br>> force !!! What is the physical justification to V_{rf} in the absence of V_c<br>> for excluded pairs?<br>> <br>> I thank you very much for your help!<br>> <br>> Pascal<br>> <br>> <br>> *******************************************************************************<br>> Pascal Baillod (PhD student) <br>> *******************************************************************************<br>> Swiss Federal Institute of Technology EPFL Tel: +41-(0)21-693-0322<br>> Institute of Chemical Sciences and Engineering , Fax: +41-(0)21-693-0320<br>> Laboratory of Computational Chemistry and Biochemistry pascal.baillod@epfl.ch<br>> Room BCH 4121, Avenue Forel, http://lcbcpc21.epfl.ch<br>> CH-1015 Lausanne <br>> *******************************************************************************<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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