[gmx-users] Re : Unusual Blow up

[Nima Soltani]

Justin Lemkul <jalemkul at ...> writes:

> 
> 
> On 9/2/15 11:59 AM, Nima Soltani wrote:
> > Justin Lemkul <jalemkul <at> ...> writes:
> >
> >>
> >>
> >> On 9/1/15 10:29 PM, Nima Soltani wrote:
> >>> Nima Soltani <nima.slt <at> ...> writes:
> >>>
> >>>>
> >>>> Thank you for your kind help dear Justin
> >>>> this is link of one of the pdb files that has been generated after
Blow up
> >>>> by Gromacs:
> >>>> https://www.dropbox.com/s/e3h05hohwp1va7p/step2170066b.pdb?dl=0
> >>>> What other types of information do I need to provide?
> >>>> Best Regards,
> >>>> Nima Soltani
> >>>> ----------------------------------------------------------
> >>>> Graduate Student of Physical Chemistry
> >>>> Department of Chemistry,
> >>>> Sharif University of Technology.
> >>>> =================================
> >>>
> >>>
> >>> excuse me
> >>> it seems that the link is broken
> >>> https://www.dropbox.com/l/WSn3CVnRZZy33coQ4QJWPp
> >>>
> >>
> >> And what does the starting structure look like?  You have lots of atoms
> > that are
> >> very close together, but I have no idea what the surface should look like.
> >>
> >> -Justin
> >>
> > I really appreciate your time that you spend helping me Justin 
> > the starting structure looks like this:
> > https://www.dropbox.com/l/qGSSN0MRJKUtJronECThnn
> > and the topology of the surface is:
> > https://www.dropbox.com/l/c0Cp7RUeuaoDGS7aSuk1Sn
> >
> > AGSS are atom types of surface ag atom
> > AGBB bulk atoms
> > AGII some virtual atom types on the surface
> > AGCC Charge associated with Drude Oscillators (connected to every AGBB &
> > AGSS through constraint)
> >
> 
> Sorry, can't spot anything out of the ordinary.  Make sure your atom types
and 
> interactions are set up properly, and if AGII are supposed to be treated as
Not Virtual in that sense! "Virtual site" is also not a good term to use :-)
they are interaction sites at the surface to direct the position of adsorbed
molecule  
> virtual sites, I see no indication of that at all in the topology.

Thank you dear Justin for everything
parameters and etc... seems to be correct except that very strange error !
it occurs after nearly 2,000,000 time-steps ,After 1 month i really do not
have any idea what is the cause of this

> 
> I also wouldn't really refer to this as a polarizable system, or that
these are 
> Drude oscillators at all; you have no [polarization] directive (or 
> alternatively, harmonic bonds) and the constraints don't allow anything to 
> oscillate at all :)  This is more of a charge-delocalization model, if
anything.

Yep, You are right, my mistake :-) 
"Including Image Charge Effects in the Molecular Dynamics
Simulations of Molecules on Metal Surfaces DOI : 10.1002/jcc.20928 "
This model is referred to as "Rod model"  

> 
> -Justin
>