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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><hr id="stopSpelling">> Date: Sat, 8 Mar 2008 23:04:46 +0100<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Coul-14, LJ-14 and RF-excl definitions (2)<br>> <br>> pascal.baillod@epfl.ch wrote:<br>> > Dear developers, <br>> > <br>> > Could somebody please tell me if I understood the following correctly (if the<br>> > statements below are correct in gromacs)?<br>> > <br>> > Excluded bonded at pairs:<br>> > <br>> > Pairs i to i+1 No non-bonded terms, all in bonded terms?<br>> > Pairs i to i+2 No non-bonded terms, all in bonded terms?<br>> > Pairs i to i+3 No non-bonded terms, all in bonded terms?<br>> > Pairs i to i+4 Coul-14 to account for bonded i to i+4 interaction?<br>> > LJ-14 to account for bonded i to i+4 interaction?<br>> <br>> This can be confusing. If you set nrexcl in your topology to 3 (default <br>> in pdb2gmx generated topologies) this is correct. In addition you have <br>> dihedral terms for 1-4 interactions of course. If you set nrexcl <br>> differently the effect will be different, and if you choose to list 1-3 <br>> interactions under the pairs section they will be computed.<br>> <br>> <br>> > <br>> > Rf-excl : Reaction field correction "Krf*Rij^2 - Crf" for ALL excluded at pairs<br>> > mentioned above? <br>> For everything in the exclusion list, independent of pairs. I'm not sure <br>> whether the Rf-excl correction takes fudgeQQ into account.<br><br>The reaction-field is not applied to pair (1-4) terms.<br>Therefore there are no issues with fudgeQQ.<br><br>Berk.<br><br>> > <br>> > For non bonded at pairs, the reaction field correction is included in the<br>> > Coul-SR and Coul-LR terms?<br>> Yes.<br>> <br>> <br>> <br>> <br>> > <br>> > I would also like to thank David van der Spoel and Xavier Periole for their very<br>> > helpful information on protein-solvent interaction energy, bringing answers<br>> > beyond expectation to my previous question!!<br>> > <br>> > Thanks a lot !!!<br>> > <br>> > Pascal <br>> > <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>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> <br>> -- <br>> David van der Spoel, Ph.D.<br>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>> spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<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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