Hi, I did read the Documentation 5 times now, but I still not get is what the shake_tol does tell me. I tried it with 10 values and can't figure out what it does. My CO bonds are constraint. Otherwise I would have bigger variations of the bond length. My .mdp file looks like this
constraints = none constraint_algorithm= shake shake_tol = 0.000005 unconstrained_start = no My question is more how I can constrain the bond length such that they vary only by a factor of +/- 0.0001. Thanks On Thu, 17 Jun 2010 08:01:04 +1000 Mark Abraham <[email protected]> wrote: > > > ----- Original Message ----- > From: Sebastian Waltz > <[email protected]> > Date: Thursday, June 17, 2010 2:23 > Subject: Re: [gmx-users] constraints bond length vari by > 10% > To: Discussion list for GROMACS users > <[email protected]> > > > Hi Mark, > > > > what I have written in the .top you can see in my first > > massage. > > OK - but my suggestion was that it was put in the wrong > *place* and I don't have enough information to say > whether that's true. > > > 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. > > I understand your frustration, but documentation can't > anticipate the answer to every question or it would be > infinitely long. That fact doesn't make it bad. What the > documentation can do is provide general instruction. If > my guess is correct, then the worked example of a .top > file in Chapter 5 will help you understand where > [constraints] needs to go. Specifically, page 109 will > point out that > > #include "ffforcefield.itp" > [ moleculetype ] > ... > [atoms] > ... > > #include "water.itp" > > [system] > ... > [molecules] > ... > > [constraints] > ... > > won't work. > > Section 5.5 has a worked example of how to use [settles] > which are a kind of constraint, and work the same way. > > Once you've worked through this information, if you still > have a problem with the documention, then a constructive > suggestion for improvement would be welcome :-) > > Mark > > > 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 -- 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
