[gmx-users] Computing the energy of a crystal unitcell

Golshan Hejazi golshan.hejazi at yahoo.com
Tue Dec 10 02:41:14 CET 2013

Thanks for your reply. 

I have a paracetamol crystal and I would like to estimate the paracetamol/paracetamol interaction per unitcell. 

To do this I am doing the following:

Energy of interaction of paracetamols per unitcell= 
Energy of a unitcell - (Energy of a molecule in the unitcell* number of the molecules in the unitcell)

Energy of interaction of paracetamols per unitcell=  Term1 + Term2

How to compute Term1: 
Took a crystal slab. Compute the total energy and divide it by the number of unitcells. The results is: -2443.29 kj/mol

How to compute Term2:
number of the molecules in the unitcell is 4. Energy of a single molecule in vacuum is 490.20 kj/mol 

Energy of interaction of paracetamols per unitcell= -2443.29 kj/mol-(-490.20*4) kj/mol= -482.378 kj/mol

Which is more than a covalent bond! 
Could you please help me to figure out what is going wrong?


On Sunday, December 8, 2013 3:49 PM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
On 2013-12-08 21:12, Golshan Hejazi wrote:
> Hello everyone,
> I am trying to compute the energy of a crystal slab using steepest decent. Learning from previous questions in the group. I am using pbc in all direction. I need to compute this energy for one layer of crystal. Since crystal unit cell vectors (a b and c) can be less than rcoulomb and rlist ... it is obvious that I receive error while generating the tpr file.
> as an example, lets assume that a=0.7, b=.9 and c=1.1 angstrom, this means if I have a crystal slab of face(100), and b and c are in XY plane, then box dimension along z axes which is equal to 0.7 ... is less than rlist ...
> how can i compute the energy of a crystal slab then? If I decrease rcoulomb and rlist ... I am introducing artifact in computing electrostatic interaction and obviously, I can not increase box dimension along Z because in that way, crystal wont be periodic along Z anymore.
> Best and thanks for you useful comments in advance
> G.
Use multiple layers and divide by the number of layers.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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