[gmx-users] Strange value for Protein-Substrate interaction

Alan Wilter Sousa da Silva alan at biof.ufrj.br
Tue Jan 14 15:07:27 CET 2003

Hi List!

	I did 2 MD of a protein + substrate under different conditions.
Protein has charge 6 and substrate 1 (total +7e).  (1) I used cut-off (1.4
nm) and no ions; and (2) with ions (PME) to vanish the total charge of my
system.  I'm interest in the energy interaction between protein/substrate
and trying to evaluate the contribution of ions.  In the MD with ions
energy values seem OK.  However when ran MD with no ions I got the strange
result below:

Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift  -kT ln<e^(E/kT)>
Coul-LR:PR-Substrate           -inf          0          0 -4.01165e+34
-4.00371e+36         nan
Total                          -inf         --         --         --
--         nan         inf

Looking MD via VMD I don't see anything spurious, substrate and Protein
keep a low RMSD, none atom traveling around the box.

Could someone, please, give some tip here?  Thanks in advance.


Alan Wilter S. da Silva
 Laboratório de Física Biológica
  Instituto de Biofísica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil

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