<br><br>----- Original Message -----<br>From: Sebastian Waltz <sebastian.waltz@physik.uni-freiburg.de><br>Date: Tuesday, June 15, 2010 22:09<br>Subject: [gmx-users] constraints bond length vari by 10%<br>To: gmx-users@gromacs.org<br><br>> Hi all,<br>> <br>> I added constraints on some bonds in my system by adding <br>> <br>> [ constraints ]<br>> ;ai aj type distance<br>> 40 41 1 0.1230<br>> 47 48 1 0.1230<br>> 54 55 1 0.1230<br>> 61 62 1 0.1230<br>> <br>> to me top file (CO double bonds) and in the mdp file <br>> <br>> constraints <br>> = none<br>> <br>> . I thought this should more or less fix my bond lengths.<br>> Nether the less the bond lengths vary by 10%. Did I make<br>> something or is it quite normal? What would be the way to<br>> fix the bond length so that they vary only by ca. 1%.<br><br>You're using the right approach, but you've probably not put your [constraints] directive in the right [moleculetype], or used the wrong .top/.itp/.tpr file at some point.<br><br>Mark