Re: question regarding warning.

From: Kwee Hong (joyssstan0202_at_gmail.com)
Date: Mon Aug 09 2010 - 21:48:14 CDT

Thanks Axel for your reply.

So is there any other way I may apply to keep my simulation running
accurately? The values I managed to obtained from my literature review would
be the bond length between the sulphur and cadmium and the relevant angles
(eg. C-S-CD, CD-S-CD). Would applying any constraint or restraint a better
choice? If yes, can you point me to any reference so that I may try to do
so.

Many thanks,
Joyce.

On Mon, Aug 9, 2010 at 6:07 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> dear joyce,
>
> On Mon, Aug 9, 2010 at 5:29 AM, Kwee Hong <joyssstan0202_at_gmail.com> wrote:
> [,,,,]
>
> > 4 cadmium ions are actually tetrahedrally bound to my protein. So, I've
> > added the below portion into the parameter file to define the bond
> between
> > the sulphur from cystein and the cadmium ion:
> >
> > SS CD 0.0000 2.4670
> >
> > The bond lenth was taken from my literature review. I leave the force
> > constant value at 0.000 as I do not find any such value in my literature
>
> if you leave a force constant at zero,
> that is the same as not defining a force at all.
>
> > review. I'm afraid that the warning might be referring to this bond
> length.
> > If so, what would be its effect to my simulation and does that mean that
> I
> > would need to make a guess on that value?
>
> there is no need to guess. each force field has
> a well laid out set of rules as to how its parameters
> are defined. typically, force constants for bonds
> can be inferred from quantum chemical vibrational
> analysis calculations. in the case of multi-valent
> metal ions, however, i would not expect too much
> accuracy, since their interactions are notoriously
> contain many-body contributions, that typical
> biomolecular forcefield only consider in an average
> way (as they are not as prevalent in bonds between
> C, N, O, H, ...).
>
> cheers,
> axel.
>
> > Thanks.
> >
> > Regards,
> > Joyce
> >
> >
> >
> >
> > On Mon, Aug 9, 2010 at 4:13 PM, Bjoern Olausson <namdlist_at_googlemail.com
> >
> > wrote:
> >>
> >> On Monday 09 August 2010 09:28:16 you wrote:
> >> > Hi everyone,
> >> >
> >> > I'm new to NAMD. While I energy minimized my system, I got a warning
> as
> >> > below in the log file:
> >> >
> >> > Warning: Ignored 12 bonds with zero force constants.
> >> >
> >> > Can anyone tell me what does that mean and how it may affect my
> >> > simulation?
> >> >
> >> > Thanks.
> >> >
> >> > Regards,
> >> > Joyce
> >>
> >> Hi,
> >>
> >> I guess you are using the TIP3 Water model with SHAKE and probably have
> 12
> >> Water molecules in your system?
> >>
> >> If this is correct, you don't have to worry about the Warning.
> >>
> >> Cheers
> >> Bjoern
> >>
> >> --
> >> Bjoern Olausson
> >> Martin-Luther-Universität Halle-Wittenberg
> >> Fachbereich Biochemie/Biotechnologie
> >> Kurt-Mothes-Str. 3
> >> 06120 Halle/Saale
> >>
> >> Phone: +49-345-55-24942
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>

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