[gmx-users] Silica Nanoparticles

[Justin Lemkul]

On 4/22/14, 11:12 AM, Kazem Sepehrinia wrote:
> Hi Dear All,
>
> Have any of you guys prepared silica nanoparticles in your Molecular
> Simulation studies? I used some open databases for obtaining of bulk
> amorphous silica file. But i'm not able to prepare silica nanoparticles.
> Once again i used materials studio glasses and made a nanoparticle but that
> one is not working also. Because i tried to minimize it and job failed. Any
> help would be greatly appreciated.
>

You'll have to define "not working" and "job failed" in more detail.  Is 
something crashing?  Are there problems with topology generation?  Using pdb2gmx 
to create a topology will likely be a major pain, since it is designed for 
(mostly) linear polymers, though g_x2top might handle it alright, provided you 
have written a suitable .n2t file.  These are all the sorts of things we need to 
know to provide useful advice.

-Justin

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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