[gmx-users] Help and thanks

Tanping Li jia_11_osu at yahoo.com
Thu Sep 8 02:12:07 CEST 2005

Hellow, evergyone,

I am analysing the interaction between a specific
residue in protein and the close waters. I use PME.

I calculated the residue-close waters by myself: 1)
use trjconv to put my residue in the center; 2) use
trjorder to order the waters by setting the residue as
reference. 3.) using q1*q2/(r*r)

GROMACS also gives me the residue-water interaction.
My result does not converge to the result from GROMACS
even if I consider all the waters within the box into
the calculation. 

My question is: does this come from the PME?
Or should I consider the periodic image of some waters
because the Columb is a long-term interaction? If it
is true, how to get the coordinates of those waters?

Thank you very much fro your help. I am confused for
several days.


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