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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><blockquote><hr id="EC_stopSpelling">Date: Sat, 17 May 2008 08:48:28 +0330<br>From: terry.b.nelson@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] [ angle_restraints_z ]<br><br>Hi all,<br>
<br>There are atoms (a1 and a2) in my small molecule coordinate file that have the same z component:<br>
a1: atom#22 (x1,y1,60.231)<br>
a2: atom#45 (x2,y2,60.231)If I use these lines only<br>
<br>
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). <br>
To restrain a1-a2 at this orientation throughout my MD calculations I included these lines to my starting topology:<br>
<br>
; Restrain the molecules wrt z-axis...<br>
[ angle_restraints_z ]<br>
; #1 #2 type theta0(degrees) k_c(kJ mpl^(-1)) multiplicity<br>
22 45 1 90 1000 1<br>
<br>
Would someone comment on:<br>
- Is this is all I need to do to restrain a1-12 wrt z-axis?<br>
- Are the above parameters (theta/K/multiplicity) reasonable/correct?<br>
- 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?<br>
<br>
Thanks.<br clear="all"><br>-- <br>Cheers,<br>Terry<br></blockquote><br>Did you look at formula 4.68 in the manual?<br>What you want is a minimum at 90 and maxima at 0 and 180.<br>So you need to use a multiplicity of 2.<br>1000 as a force constant seems too large to me, this means that<br>the 0/180 degrees is penalized by 2000 kJ/mol.<br><br>Berk.<br><br><blockquote>
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