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<br><br>> Date: Thu, 28 May 2009 21:49:45 +1000<br>> From: Mark.Abraham@anu.edu.au<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] constant term in dihedral potential function<br>> <br>> Kukol, Andreas wrote:<br>> > Hi,<br>> > <br>> > I supply the multiple dihedral terms as a combination of single ones, such as:<br>> > <br>> > ;atom no. type phis k mult<br>> > 22 23 24 25 1 180 7.470 1<br>> > 22 23 24 25 1 0 3.900 2<br>> > 22 23 24 25 1 180 1.100 3<br>> > 22 23 24 25 1 90 -5.685 0<br>> <br>> I don't believe this works in the way you might expect. Page 109 of the <br>> manual contradicts me, but (undocumented) dihedral type 9 was added <br>> recently to allow multiple strictly-consecutive dihedrals of type "1" to <br>> be accumulated on the same atoms. Anyway, this can readily be checked by <br>> comparing 0-step EM runs, before and after commenting out the last of <br>> the multiple dihedrals pre-grompp. Also, you can look at a gmxdump of <br>> the .tpr.<br><br>This works fine.<br><br>> <br>> > In case I supply the potential with a Ryckaert-Bellemans dihedral, do I need to exclude the 1-4 interactions between atoms 22 and 25 ?<br>> <br>> The form of the dihedral function doesn't matter. See section 5.4 of the <br>> manual.<br><br>If you set up the dihedral potential yourself, you choose if to use 1-4 or not.<br>Your own force-field setup determines if to use 1-4's or not, not the technical way<br>you supply the potentials in the topology.<br><br>> <br>> > Maybe one Ryckaert-Bellemans dihedral would be also computationally more efficient ?<br>> <br>> Maybe.<br><br>Yes, RB will be computationally more efficient, but the time spent on it is probably negligible.<br><br>Berk<br><br>> <br>> Mark<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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