[gmx-users] Coulomb (SR) problem

Thanasis Koukoulas koukoulas_th at yahoo.gr
Fri Jun 11 12:13:20 CEST 2010

hello again

I had a problem with a sim of some molecules in vacuum and a gmx-user told me to do a simulation only in one molecule just to see what gromacs calculates and what does not. My problem concerned the sum of all energies in the system. After i did the sim with one molecule i found out that either gromacs either me calculate the Coulomb SR(short range) energy wrong. so for step 0 of this simulation I had this result:

Started mdrun on node 0 Fri Jun 11 12:52:33 2010

           Step           Time         Lambda
              0        0.00000        0.00000

Grid: 3 x 3 x 3 cells
Long Range LJ corr.: <C6> 3.8522e-03
Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091
   Energies (kJ/mol)
          Angle Ryckaert-Bell.          LJ-14     Coulomb-14        LJ (SR)
    5.70627e+00    8.37083e+00    6.80805e-03    1.72679e+02   -3.25801e+00
  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
   -7.32091e-03   -2.93587e+01   -1.21273e+02    3.28661e+01    3.94838e+01
   Total Energy    Temperature Pressure (bar)  Cons. rmsd ()
    7.23499e+01    3.65291e+02    4.25496e+01    3.53180e-07

so as you can see the value of  Coulomb (SR) is
-2.93587e+01 and my calculation is 

I believe that even i have done wrong calculations the value that gromacs finds is not correct. 
I found this value from the formula sum(f*qi*qj/rij) for every atom pair like
1-2,1-3,(not the 1-4),1-5....etc 2-3,2-4(not 1-2 because it is already calculated) ....etc ...3-.....etc......... inside the rcoulomb (the whole molecule)
where f is the electric conversion factor f=138,935kJmol-1*nm*e-2
IS COULOMB (SR) calculated that way by hand??? i an using PME btw

i have not done arithmetic mistake i am sure for that (at least :) )
Please consider that:
1) I dont use ffXXX.itp libraries from gromacs i have my own
2) I have tried every possible way to do this simulation for the past 3 months (its my problem i know that !!! :) )
3) I have calculated the coulomb 1-4 with success and great accuracy
4) I have also caclulated the LJ (SR) with success (irrelevant!!!) :)
5) i am using  gromacs 4.05

Please if you have smth to advise me about this simulation except committing suicide  of course :) please feel free to do it

Thanks in advance

especially  Mark Abraham who helped my at first place

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