[gmx-users] constraints bond length vari by 10%

[Sebastian Waltz]

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 <mark.abraham at anu.edu.au> wrote:
> 
> 
> ----- Original Message -----
> From: Sebastian Waltz
> <sebastian.waltz at physik.uni-freiburg.de>
> Date: Thursday, June 17, 2010 18:59
> Subject: Re: [gmx-users] constraints bond length vari by
> 10%
> To: Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> 
> > 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 <mark.abraham at anu.edu.au> wrote:
> > > 
> > > 
> > > ----- Original Message -----
> > > From: Sebastian Waltz
> > > <sebastian.waltz at physik.uni-freiburg.de>
> > > Date: Thursday, June 17, 2010 2:23
> > > Subject: Re: [gmx-users] constraints bond length vari
> by
> > > 10%
> > > To: Discussion list for GROMACS users
> > > <gmx-users at gromacs.org>
> > > 
> > > > 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 <mark.abraham at anu.edu.au> wrote:
> > > > > 
> > > > > 
> > > > > ----- Original Message -----
> > > > > From: Sebastian Waltz
> > > > > <sebastian.waltz at physik.uni-freiburg.de>
> > > > > Date: Tuesday, June 15, 2010 22:09
> > > > > Subject: [gmx-users] constraints bond length vari
> by
> > > 10%
> > > > > To: gmx-users at gromacs.org
> > > > > 
> > > > > > 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
> > > > > 
> > > > 
> > > > -- 
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