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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>I think you do not want to distinguish between parallel and anti-parallel.<br>But in your case using multiplicity 1 or 2 does not matter much.<br></div>1000 kJ/mol makes the orientation extremely rigid, but I don't know<br>how rigid you want to have it.<br>100 kJ/mol is probably a more reasonable order of magnitude.<br><br>Berk<br><br><br><blockquote><hr id="EC_stopSpelling">Date: Tue, 20 May 2008 16:39:22 +0430<br>From: terry.b.nelson@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: Re: [gmx-users] [ angle_restraints_z ]<br><br>Dear Berk,<br><br>Thanks for the reply.<br> <br>Yes. In fact I made the choice of multiplicity=1 based on the explanation in eq. 4.68:<br><br>"A multiplicity (n) of 2 is useful when you do not want to distinguish between parallel and anti-parallel vectors."<br>
<br>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. <br><br>Please correct me if I am missing something.<br><br>If multiplicity 1 is OK do you still think that the force constant 1000 kJ/mo is too large in my system?<br>
<br><br><div class="EC_gmail_quote">On Mon, May 19, 2008 at 5:34 PM, Berk Hess <<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>> wrote:<br><blockquote class="EC_gmail_quote" style="padding-left: 1ex;">
<div><div style="text-align: left;"><br></div><br><br><br><blockquote><hr>Date: Sat, 17 May 2008 08:48:28 +0330<br>From: <a href="mailto:terry.b.nelson@gmail.com">terry.b.nelson@gmail.com</a><br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Subject: [gmx-users] [ angle_restraints_z ]<div><div></div><div class="EC_Wj3C7c"><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></div></div></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><font color="#888888"><br>Berk.<br></font><div class="EC_WgoR0d"><br><blockquote>
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