I don't who does not get it right. My constraints work and it does change when I comment out the constraints. I put the constraints right there they write it in the Documentation. I do not even include water.itp. My question is how I can constrain the bonds more rigid. And for this I would like to know what does the shake_tol means.
Thanks On Fri, 18 Jun 2010 09:37:36 +1000 Mark Abraham <[email protected]> wrote: > > > ----- Original Message ----- > From: Sebastian Waltz > <[email protected]> > Date: Thursday, June 17, 2010 18:59 > Subject: Re: [gmx-users] constraints bond length vari by > 10% > To: Discussion list for GROMACS users > <[email protected]> > > > 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. > > The above is fine, except that your topology probably has > no constraints defined in it, because your [constraints] > is in the wrong place. Try commenting out the contents of > your constraints directive and see if you get identical > results. This is the last time I'm going to repeat > myself, since you're appearing to ignore my feedback :-) > > Mark > > > 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 -- 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
