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<br><br>> Date: Sat, 17 Apr 2010 14:58:22 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] manual eq. 4.74-4.75 (dihedral restraints) head scratcher<br>> <br>> <br>> <br>> Daniel L. Ensign wrote:<br>> > Hello gmx-users, you rock and rollers,<br>> > <br>> > Equations 4.74 and 4.75 in my copy of the manual have (please pardon my <br>> > pseudo-LaTeX):<br>> > <br>> > (4.74)<br>> > \phi' = (\phi - \phi_0) MOD 2\pi<br>> > <br>> > (4.75)<br>> > V(\phi') = \frac{1}{2}k ( \phi' - \phi_0 - \Delta \phi )^2 if \phi' > <br>> > \Delta \phi<br>> > or<br>> > V(\phi') = 0 if \phi' \leq \Delta \phi<br>> > <br>> > but should there be absolute values around all of the \phi-\phi_0? Which <br>> > way is it in the code -- with the absolute distance between \phi and <br>> > \phi_0 or the directed distance?<br>> > <br>> <br>> It looks like absolute values are considered. From src/gmxlib/dihres.c:<br>> <br>> /* phi can jump if phi0 is close to Pi/-Pi, which will cause huge<br>> * force changes if we just apply a normal harmonic.<br>> * Instead, we first calculate phi-phi0 and take it modulo (-Pi,Pi).<br>> * This means we will never have the periodicity problem, unless<br>> * the dihedral is Pi away from phiO, which is very unlikely due to<br>> * the potential.<br>> */<br>> dp = phi-phi0;<br>> if (fabs(dp) > dphi) {<br>> /* dp cannot be outside (-2*pi,2*pi) */<br>> if (dp >= M_PI)<br>> dp -= 2*M_PI;<br>> else if(dp < -M_PI)<br>> dp += 2*M_PI;<br>> <br>> <br>> > Also, as far as I can tell (and some mornings I definitely don't read <br>> > too good) neither the manual nor <br>> > http://wiki.gromacs.org/index.php/Dihedral_Restraints define the fields <br>> > in [ dihedral_restraints ], although the latter does name them. There, I <br>> > see<br>> > <br>> > [ dihedral_restraints ]<br>> > ; ai aj ak al type label phi dphi kfac power<br>> > 5 7 9 15 1 1 180 0 1 2<br>> > <br>> > ai, aj, ak, al = atom numbers, obviously<br>> > type = ?, but I'm guessing there's only one type anyway<br>> <br>> Probably so.<br>> <br>> > label = what is this one?<br>> <br>> Looks to be bookkeeping. The code doesn't seem to use it other than to print <br>> debug information, but I could be wrong since I haven't surfed around it very long.<br>> <br><br>power and label have been copied from distance restraints, but not used at all.<br>I have already removed them for the next release.<br><br>Berk<br><br>> > phi means phi0 ?<br>> <br>> Yes.<br>> <br>> > dphi means Delta phi, I guess<br>> <br>> Yes.<br>> <br>> > kfac is the force constant, probably<br>> <br>> Indirectly. This term is equivalent to the fac value in distance restraints. <br>> Since the force constant is specified in the .mdp file, different restraints <br>> would otherwise have to be restrained with equivalent force constants. The <br>> value of kfac is multiplied by the value of dihre_fc in the .mdp file, so that <br>> different restraints could have different force constants.<br>> <br>> > power = what is this one? Does 2 give me harmonic constraints?<br>> > <br>> <br>> Not a clue on this one. Also doesn't seem to be used in the code, but maybe <br>> it's somewhere outside of dihres.c.<br>> <br>> > I'd be happy to translate any answers given to the wiki, assuming I get <br>> > answered and that I'm allowed to edit the wiki.<br>> > <br>> <br>> The wiki link you posted above doesn't actually exist any more, and actually <br>> points to an empty page, even though the content is still online:<br>> <br>> http://www.gromacs.org/index.php?title=Documentation/How-tos/Dihedral_Restraints<br>> <br>> The old wiki doesn't actually exist, but has been merged into the Gromacs site, <br>> so if you register as a user you can make contributions. If you have troubles, <br>> I might get around to updating this page with the above information, unless <br>> there is more information to be considered, or I'm wrong :)<br>> <br>> -Justin<br>> <br>> > May the Force be with you (as long as it's calculated in hand-tuned <br>> > assembly loops),<br>> > Dan<br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.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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