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

[Mark Abraham]

----- 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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