[gmx-users] pdb information

Justin Lemkul jalemkul at vt.edu
Tue Dec 30 16:38:28 CET 2014

On 12/30/14 1:48 AM, elham tazikeh wrote:
> Dear Justin
> i choosed *Cubic* box for amyloid beta peptide+Zn ion simulation
> for this reason, my *volume* is defined

Sure, but box shape doesn't mean anything.  Box volume is what is important.  I 
can make a cubic box with 1-nm edges and I can make a box with 100000-nm edges; 
they're both cubic but that fact tells you nothing about the volume.

> if i suppose that, Zn ion = 1 mol

Well, it's one molecule, not 1 mol.

> its concentration will be calculated
> my assumption is correct?

I have no idea what this means.  It's absolutely trivial to convert between a 
number of particles (in this case, 1) and a volume in nm^3 to a concentration. 
It's simple unit transformation - consult any basic chemistry textbook.



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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