[gmx-users] Re : Unusual Blow up

[Nima Soltani]

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)

-Nima