[gmx-users] calculating com-com distances.
fernando.cesar.lf at gmail.com
Sun Apr 12 14:10:43 CEST 2009
Is there the possibility of the g_dist program don't provide the correct
com-com distances for molecules simulated in triclinic cells
under anisotropic pressure?
(I've been calculating com-com distances in order to study the clustering of
lipids self-assembled. For it, I've written a simple
code reads coordinates, calculate com positions, make the 26 images for each
one and verify the smallest distance between com(lipid A)
and com(lipid B) among all the 27 combinations. In 63% of all lipid-lipid
combinations, the distances obtained for both programs are
equal and others 20% my code obtains smaller values. For the calculations
I've obtained the vectors for the rectangular box in g_energy,
using Box_XX, Box_YY and Box_ZZ options; I didn't use the vectors of the
Fernando C. Lopes F., PhD student
Department of Physics
UNESP - São Paulo State University
15054-000 São José do Rio Preto, São Paulo, Brazil
e-mail: ffilho at ibilce.unesp.br
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