[gmx-users] refcoord-scaling

[Chetan Mahajan]

Hi Mark

We discussed this "refcoord scaling=com not working" quite a bit. With new
version of gromacs 4.6.5, it seemed that com option is working fine.
However, I later found out that it is only for equilibration run and system
does blow up (domain decomposition error) in production run. Again to
revise: I have a system consisting of 13133 atoms ( A TiO2 crystal ( 720
Ti) , 3656 water molecules, 1 formate ion, 1 sodium ion). Atoms in TiO2
crystal are held by position restraints.

In the following you had made a comment that multiple COM and PBC may not
be working well with each other. WHy did you think it's a case of
"multiple" com of TiO2?  I am asking this, since in my TiO2 crystal, we are
not defining any bonds between Ti and O, although we are defining entire
TiO2 crystal to be one molecule. So, we can think of only 1 com.

Thanks
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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