[gmx-users] Re : Unusual Blow up

Justin Lemkul jalemkul at vt.edu
Wed Sep 2 22:52:42 CEST 2015

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 
virtual sites, I see no indication of that at all in the topology.

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.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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