[gmx-users] Positive Total energy

Thanasis Koukoulas koukoulas_th at yahoo.gr
Tue Jun 15 16:43:32 CEST 2010


hi

I did what you said to me but with a new system about 450 molecules in vacuum  because i was given an equilibrated  initial configuration. I also did a simulation with one molecule in vacuum just to compare.

Simulation from 450 molecules with C12 = 3.325789e-7

 Step           Time         Lambda
              0        0.00000        0.00000

Grid: 6 x 6 x 6 cells
Long Range LJ corr.: <C6> 4.0328e-03
Long Range LJ corr.: Epot   -654.408, Pres:   -143.188, Vir:    654.408
   Energies (kJ/mol)
          Angle Ryckaert-Bell.          LJ-14     Coulomb-14        LJ (SR)
    6.80661e+03    1.21531e+04    9.48296e+02    9.31284e+04   -2.41886e+04
  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
   -6.54408e+02   -4.41319e+04   -5.98995e+04   -1.58379e+04    1.62374e+04
   Total Energy    Temperature Pressure (bar)  Cons. rmsd ()
    3.99498e+02    2.99364e+02   -6.26115e+01    1.26990e-06

Simulation from 450 molecules with C12 =0.000000325789

 Step           Time         Lambda
              0        0.00000        0.00000

Grid: 6 x 6 x 6 cells
Long Range LJ corr.: <C6> 4.0328e-03
Long Range LJ corr.: Epot   -654.408, Pres:   -143.188, Vir:    654.408
   Energies (kJ/mol)
          Angle Ryckaert-Bell.          LJ-14     Coulomb-14        LJ (SR)
    6.80661e+03    1.21531e+04    9.68060e+02    9.31284e+04   -2.41886e+04
  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
   -6.54408e+02   -4.41319e+04   -5.98995e+04   -1.58181e+04    1.62374e+04
   Total Energy    Temperature Pressure (bar)  Cons. rmsd ()
    4.19256e+02    2.99364e+02   -5.21517e+01    1.24989e-06

Simulation from 450 molecules with [pairs] line which includes C12=3.8522e-03
 commented out
Step           Time         Lambda
              0        0.00000        0.00000

Grid: 6 x 6 x 6 cells
Long Range LJ corr.: <C6> 4.0328e-03
Long Range LJ corr.: Epot   -654.408, Pres:   -143.188, Vir:    654.408
   Energies (kJ/mol)
          Angle Ryckaert-Bell.          LJ-14     Coulomb-14        LJ (SR)
    6.80661e+03    1.21531e+04    0.00000e+00    9.31284e+04   -2.41886e+04
  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
   -6.54408e+02   -4.41319e+04   -5.98995e+04   -1.67862e+04    1.62403e+04
   Total Energy    Temperature Pressure (bar)  Cons. rmsd ()
   -5.45867e+02    2.99418e+02   -5.84485e+02    1.26484e-06
 
this simulation endf with a fatal error:

Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.


Now for the simulations with only one molecule :


Simulation from 1 molecule with C12 = 3.325789e-7

 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
Simulation from 1 molecule with C12 =0.000000325789
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    3.29260e+01    3.94842e+01
   Total Energy    Temperature Pressure (bar)  Cons. rmsd ()
    7.24102e+01    3.65295e+02    4.25882e+01    3.19025e-07
Simulation from 1 molecule with [pairs] line which includes C12=3.8522e-03 commented out
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    0.00000e+00    1.72679e+02   -3.25801e+00
  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
   -7.32091e-03   -2.93587e+01   -1.21273e+02    3.28593e+01    3.94837e+01
   Total Energy    Temperature Pressure (bar)  Cons. rmsd ()
    7.23430e+01    3.65290e+02    4.25426e+01    3.53180e-07
As you can see Coulomb-1.4 has the same value = 1.72679e+02 and it is the almost the same I found calculating by hand = 171.9770708. I also calculated 
LJ14 by hand and i found 0.00751 though the value of LJ14 from gromacs is 0.006808 close but not the same!

In this email i have attached the results from gmxdump -s topol.tpr | less
for both of the systems. I also send you the grompp.mdp file i use.

thanks



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