[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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100615/cee344a0/attachment.html>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: topol.tpr_1_molecule.txt
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100615/cee344a0/attachment.txt>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: topol.tpr_450_molecules.txt
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100615/cee344a0/attachment-0001.txt>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: grompp.mdp
Type: application/octet-stream
Size: 7860 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100615/cee344a0/attachment.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ciej_one.gro
Type: application/octet-stream
Size: 683 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100615/cee344a0/attachment-0001.obj>
More information about the gromacs.org_gmx-users
mailing list