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

Berk Hess gmx3 at hotmail.com
Fri Jun 18 10:15:07 CEST 2010 

Hi,

shake_tol sets the relative tolerance of the constraint lengths.
This means that the constraints should not differ more than +-shake_tol
after constraining: for example a constraint of length 0.1 nm with shake_tol=1e-4
should be between 0.09999 and 0.10001 nm.

Note that the settings in your last mail are quite close to the floating point precision.
Double precision could help in that case.
But your earlier mails also seem to indicate problems with lower shake_tols.
I have no clue what could be wrong in that case.

BTW have you tried LINCS?

Berk

> From: sebastian.waltz at physik.uni-freiburg.de
> Subject: Re: [gmx-users] constraints bond length vari by 10%
> To: gmx-users at gromacs.org
> Date: Fri, 18 Jun 2010 09:20:05 +0200
> 
> 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
> > > > > > 
> > > > > 
> > > > > -- 
> > > > > gmx-users mailing list    gmx-users at gromacs.org
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