[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
-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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