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

[Sebastian Waltz]

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 <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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