Hi Mark, what I have written in the .top you can see in my first massage. I actually don't know what to write what and in which .itp/.tpr file I have to add something and I also can't find something in the Internet. The documentation for the constraints is just bad.
Thanks Sebsatian On Wed, 16 Jun 2010 09:05:20 +1000 Mark Abraham <[email protected]> wrote: > > > ----- Original Message ----- > From: Sebastian Waltz > <[email protected]> > Date: Tuesday, June 15, 2010 22:09 > Subject: [gmx-users] constraints bond length vari by 10% > To: [email protected] > > > Hi all, > > > > I added constraints on some bonds in my system by > adding > > > > [ constraints ] > > ;ai aj type distance > > 40 41 1 0.1230 > > 47 48 1 0.1230 > > 54 55 1 0.1230 > > 61 62 1 0.1230 > > > > to me top file (CO double bonds) and in the mdp file > > > > constraints > > = none > > > > . I thought this should more or less fix my bond > lengths. > > Nether the less the bond lengths vary by 10%. Did I > make > > something or is it quite normal? What would be the way > to > > fix the bond length so that they vary only by ca. 1%. > > 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. > > Mark > -- gmx-users mailing list [email protected] http://lists.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
