[gmx-users] refcoord-scaling

[Chetan Mahajan]

Thanks, Mark. So is 'all' option okay when positions of each of the atoms
of TiO2 crystal (2160 atoms total) are restrained in space? Apparently, it
does not seem correct, since positions of the atoms of TiO2 crystal change
when 'all' option is applied. However, it does not give error as 'com'
option does.

regards
Chetan


On Mon, Mar 24, 2014 at 11:16 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> On Mon, Mar 24, 2014 at 4:44 PM, Chetan Mahajan <chetanvm10 at gmail.com
> >wrote:
>
> > Hi Mark,
> >
> > I am restraining positions of each of the atoms of TiO2 crystal. Could
> you
> > comment again why should simulation crash when 'com' option is used
> against
> > 'all' option?
>
>
> Don't know, I'd have to read the code, and I don't care enough to do that
> :-) But if you had a molecule whose COM might cross PBC while
> equilibrating, and the implementation had some limitation that was
> described with "only one COM is used, even when there are multiple
> molecules" then I'd be expecting problems.
>
>
> > Also, description in the manual does not answer my question:
> > when is 'all' option generally used? When is 'com' option generally used?
> > When is 'no' option generally used?
> >
>
> When they work for your case. But they are all hacks for doing something
> artificial, like getting a system equilibrated. When and why would depend
> on things like how many restrained sites per molecule, how rigid the model
> of the molecule  was..
>
> Mark
>
>
> >
> > Thanks!
> >
> > regards
> > Chetan
> >
> >
> > On Mon, Mar 24, 2014 at 4:16 AM, Mark Abraham <mark.j.abraham at gmail.com
> > >wrote:
> >
> > > On Mar 24, 2014 1:10 AM, "Chetan Mahajan" <chetanvm10 at gmail.com>
> wrote:
> > > >
> > > > Dear all:
> > > >
> > > > I am trying to get a simulation of water solvated titanium oxide
> > running.
> > > > When 'all' option is used for refcoord-scaling, simulation runs ok.
> > > > However, when 'com' option is used for refcoord-scaling, simulation
> > > crashes
> > > > with any of the following errors. Could anyone explain to me why is
> > this
> > > > happening
> > >
> > > See the description of com. You didn't tell us what you were
> restraining,
> > > so it's hard to help. But I can see multiple com of tio2 and PBC not
> > > working well together, particularly if you box size is far from best.
> > >
> > > > or when each of the options such as 'all', 'com' and 'no' is used?
> > >
> > > When you really care about your starting position and need to
> equilibrate
> > > in NPT.
> > >
> > > Mark
> > >
> > > > Thanks a lot!
> > > > regards
> > > > Chetan
> > > >
> > > >
> > > > Errors:
> > > >
> > > > X particles communicated to PME node Y are more than a cell length
> out
> > of
> > > > the domain decomposition cell of their charge group
> > > >
> > > > This is another way that mdrun tells you your system is blowing
> > > > up<http://www.gromacs.org/Documentation/Terminology/Blowing_Up>.
> > > > In GROMACS version 4.0, domain decomposition was introduced to divide
> > the
> > > > system into regions containing nearby atoms (for more details, see
> the
> > > > manual <http://www.gromacs.org/Documentation/Manual> or the GROMACS
> 4
> > > > paper<http://dx.doi.org/10.1021/ct700301q>).
> > > > If you have particles that are flying across the system, you will get
> > > this
> > > > fatal error. The message indicates that some piece of your system is
> > > > tearing apart (hence out of the "cell of their charge group"). Refer
> > > > to the Blowing
> > > > Up <http://www.gromacs.org/Documentation/Terminology/Blowing_Up>
> page
> > > for
> > > > advice on how to fix this issue.
> > > >
> > > >
> > > > A charge group moved too far between two domain decomposition steps.
> > > > --
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