Dear Berk, Thanks for the reply.
Yes. In fact I made the choice of multiplicity=1 based on the explanation in eq. 4.68: "A multiplicity (n) of 2 is useful when you do not want to distinguish between parallel and anti-parallel vectors." Since my molecule is slightly polar and it may matter whether it is at 0 or 180 orientation, I decided to use multiplicity of 1. Please correct me if I am missing something. If multiplicity 1 is OK do you still think that the force constant 1000 kJ/mo is too large in my system? On Mon, May 19, 2008 at 5:34 PM, Berk Hess <[EMAIL PROTECTED]> wrote: > > > > > ------------------------------ > Date: Sat, 17 May 2008 08:48:28 +0330 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] [ angle_restraints_z ] > > > Hi all, > > There are atoms (a1 and a2) in my small molecule coordinate file that have > the same z component: > a1: atom#22 (x1,y1,60.231) > a2: atom#45 (x2,y2,60.231)If I use these lines only > > Therefore the vector a1-a2 makes theta=90o with the z-axis. in my previous > MD runs the a1-a2 were flexible (theta was observed in the range of 30-120 > degrees). > To restrain a1-a2 at this orientation throughout my MD calculations I > included these lines to my starting topology: > > ; Restrain the molecules wrt z-axis... > [ angle_restraints_z ] > ; #1 #2 type theta0(degrees) k_c(kJ mpl^(-1)) multiplicity > 22 45 1 90 1000 1 > > Would someone comment on: > - Is this is all I need to do to restrain a1-12 wrt z-axis? > - Are the above parameters (theta/K/multiplicity) reasonable/correct? > - with this I should expect a1 and a2 stay in xy-plane (with their z > component equal at each frame) during minimization, equilibration and > production? > > Thanks. > > -- > Cheers, > Terry > > > Did you look at formula 4.68 in the manual? > What you want is a minimum at 90 and maxima at 0 and 180. > So you need to use a multiplicity of 2. > 1000 as a force constant seems too large to me, this means that > the 0/180 degrees is penalized by 2000 kJ/mol. > > Berk. > > > ------------------------------ > Express yourself instantly with MSN Messenger! MSN > Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 > -- Cheers, Terry
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