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 -1302.68 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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