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
ntypes=41
functype[0]=LJ_SR, c6= 9.06379987e-03, c12= 2.52059999e-05
functype[1]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05
functype[2]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06
functype[3]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06
functype[4]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[5]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05
functype[6]=LJ_SR, c6= 5.81080001e-03, c12= 2.20710008e-05
functype[7]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06
functype[8]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06
functype[9]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[10]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06
functype[11]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06
functype[12]=LJ_SR, c6= 8.81469983e-04, c12= 4.24770008e-07
functype[13]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07
functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[15]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06
functype[16]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06
functype[17]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07
functype[18]=LJ_SR, c6= 2.34650006e-03, c12= 1.78020002e-06
functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[20]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[22]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[23]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[24]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[25]=ANGLES, thA= 1.14000e+02, ctA= 5.19650e+02, thB=
1.14000e+02, ctB= 5.19650e+02
functype[26]=ANGLES, thA= 1.12000e+02, ctA= 4.18220e+02, thB=
1.12000e+02, ctB= 4.18220e+02
functype[27]=ANGLES, thA= 1.12000e+02, ctA= 5.02190e+02, thB=
1.12000e+02, ctB= 5.02190e+02
functype[28]=ANGLES, thA= 1.09470e+02, ctA= 4.19050e+02, thB=
1.09470e+02, ctB= 4.19050e+02
functype[29]=ANGLES, thA= 1.08500e+02, ctA= 4.60620e+02, thB=
1.08500e+02, ctB= 4.60620e+02
functype[30]=RBDIHS, rbcA[0]= 8.23107815e+00, rbcA[1]= 1.69526253e+01,
rbcA[2]= 1.13392794e+00, rbcA[3]=-2.63176327e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 8.23107815e+00, rbcB[1]= 1.69526253e+01, rbcB[2]= 1.13392794e+00,
rbcB[3]=-2.63176327e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[31]=RBDIHS, rbcA[0]= 6.98307610e+00, rbcA[1]= 1.77361813e+01,
rbcA[2]= 8.86987984e-01, rbcA[3]=-2.56062469e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 6.98307610e+00, rbcB[1]= 1.77361813e+01, rbcB[2]= 8.86987984e-01,
rbcB[3]=-2.56062469e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[32]=RBDIHS, rbcA[0]= 7.94905090e+00, rbcA[1]= 7.89251280e+00,
rbcA[2]= 2.72299004e+00, rbcA[3]=-1.85645523e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 7.94905090e+00, rbcB[1]= 7.89251280e+00, rbcB[2]= 2.72299004e+00,
rbcB[3]=-1.85645523e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[33]=RBDIHS, rbcA[0]= 8.36826706e+00, rbcA[1]= 2.51047993e+01,
rbcA[2]= 4.18417501e+00, rbcA[3]=-3.34730682e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 8.36826706e+00, rbcB[1]= 2.51047993e+01, rbcB[2]= 4.18417501e+00,
rbcB[3]=-3.34730682e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[34]=RBDIHS, rbcA[0]= 2.82201505e+00, rbcA[1]= 2.94307399e+00,
rbcA[2]= 4.85065997e-01, rbcA[3]=-6.25015497e+00, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 2.82201505e+00, rbcB[1]= 2.94307399e+00, rbcB[2]= 4.85065997e-01,
rbcB[3]=-6.25015497e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[35]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B=
0.00000000e+00, c12B= 0.00000000e+00
functype[36]=LJC14_Q, fqq= 0.00000000e+00, qi= 0.00000000e+00, qj=
0.00000000e+00, c6= 0.00000000e+00, c12= 3.32578907e-07
functype[37]=CONSTR, dA= 1.53999999e-01, dB= 1.53999999e-01
functype[38]=CONSTR, dA= 9.44999978e-02, dB= 9.44999978e-02
functype[39]=CONSTR, dA= 1.43000007e-01, dB= 1.43000007e-01
functype[40]=CONSTR, dA= 1.41000003e-01, dB= 1.41000003e-01
fudgeQQ = 0.5
ntypes=41
functype[0]=LJ_SR, c6= 9.06379987e-03, c12= 2.52059999e-05
functype[1]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05
functype[2]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06
functype[3]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06
functype[4]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[5]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05
functype[6]=LJ_SR, c6= 5.81080001e-03, c12= 2.20710008e-05
functype[7]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06
functype[8]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06
functype[9]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[10]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06
functype[11]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06
functype[12]=LJ_SR, c6= 8.81469983e-04, c12= 4.24770008e-07
functype[13]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07
functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[15]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06
functype[16]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06
functype[17]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07
functype[18]=LJ_SR, c6= 2.34650006e-03, c12= 1.78020002e-06
functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[20]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[22]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[23]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[24]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[25]=ANGLES, thA= 1.14000e+02, ctA= 5.19650e+02, thB=
1.14000e+02, ctB= 5.19650e+02
functype[26]=ANGLES, thA= 1.12000e+02, ctA= 4.18220e+02, thB=
1.12000e+02, ctB= 4.18220e+02
functype[27]=ANGLES, thA= 1.12000e+02, ctA= 5.02190e+02, thB=
1.12000e+02, ctB= 5.02190e+02
functype[28]=ANGLES, thA= 1.09470e+02, ctA= 4.19050e+02, thB=
1.09470e+02, ctB= 4.19050e+02
functype[29]=ANGLES, thA= 1.08500e+02, ctA= 4.60620e+02, thB=
1.08500e+02, ctB= 4.60620e+02
functype[30]=RBDIHS, rbcA[0]= 8.23107815e+00, rbcA[1]= 1.69526253e+01,
rbcA[2]= 1.13392794e+00, rbcA[3]=-2.63176327e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 8.23107815e+00, rbcB[1]= 1.69526253e+01, rbcB[2]= 1.13392794e+00,
rbcB[3]=-2.63176327e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[31]=RBDIHS, rbcA[0]= 6.98307610e+00, rbcA[1]= 1.77361813e+01,
rbcA[2]= 8.86987984e-01, rbcA[3]=-2.56062469e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 6.98307610e+00, rbcB[1]= 1.77361813e+01, rbcB[2]= 8.86987984e-01,
rbcB[3]=-2.56062469e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[32]=RBDIHS, rbcA[0]= 7.94905090e+00, rbcA[1]= 7.89251280e+00,
rbcA[2]= 2.72299004e+00, rbcA[3]=-1.85645523e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 7.94905090e+00, rbcB[1]= 7.89251280e+00, rbcB[2]= 2.72299004e+00,
rbcB[3]=-1.85645523e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[33]=RBDIHS, rbcA[0]= 8.36826706e+00, rbcA[1]= 2.51047993e+01,
rbcA[2]= 4.18417501e+00, rbcA[3]=-3.34730682e+01, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 8.36826706e+00, rbcB[1]= 2.51047993e+01, rbcB[2]= 4.18417501e+00,
rbcB[3]=-3.34730682e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[34]=RBDIHS, rbcA[0]= 2.82201505e+00, rbcA[1]= 2.94307399e+00,
rbcA[2]= 4.85065997e-01, rbcA[3]=-6.25015497e+00, rbcA[4]= 0.00000000e+00,
rbcA[5]= 0.00000000e+00
rbcB[0]= 2.82201505e+00, rbcB[1]= 2.94307399e+00, rbcB[2]= 4.85065997e-01,
rbcB[3]=-6.25015497e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
functype[35]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B=
0.00000000e+00, c12B= 0.00000000e+00
functype[36]=LJC14_Q, fqq= 0.00000000e+00, qi= 0.00000000e+00, qj=
0.00000000e+00, c6= 0.00000000e+00, c12= 3.32578907e-07
functype[37]=CONSTR, dA= 1.53999999e-01, dB= 1.53999999e-01
functype[38]=CONSTR, dA= 9.44999978e-02, dB= 9.44999978e-02
functype[39]=CONSTR, dA= 1.43000007e-01, dB= 1.43000007e-01
functype[40]=CONSTR, dA= 1.41000003e-01, dB= 1.41000003e-01
fudgeQQ = 0.5
grompp.mdp
Description: Binary data
ciej_one.gro
Description: Binary data
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