[gmx-users] Re: Energy miscalculation
Thanasis Koukoulas
koukoulas_th at yahoo.gr
Mon Jun 21 13:21:29 CEST 2010
2) deleting the [pairs] and all the lines below
I)from md.log
Step Time Lambda 0 0.00000 0.00000
Grid: 3 x 3 x 3 cellsLong Range LJ corr.: <C6> 3.8522e-03Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091 Energies (kJ/mol) Angle Ryckaert-Bell. LJ (SR) Disper. corr. Coulomb (SR) 5.70628e+00 8.37083e+00 -3.25801e+00 -7.32091e-03 -2.93587e+01 Coul. recip. Potential Kinetic En. Total Energy Temperature -1.21273e+02 -1.39819e+02 3.94033e+01 -1.00416e+02 3.64546e+02 Pressure (bar) Cons. rmsd () 3.09781e+01 3.89303e-07
II) from gmxdump
ffparams: atnr=5 ntypes=39 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+00functype[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+00rbcB[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+00rbcB[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+00rbcB[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+00rbcB[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+00rbcB[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]=CONSTR, dA= 1.53999999e-01, dB= 1.53999999e-01 functype[36]=CONSTR, dA= 9.44999978e-02, dB= 9.44999978e-02 functype[37]=CONSTR, dA= 1.43000007e-01, dB= 1.43000007e-01 functype[38]=CONSTR, dA= 1.41000003e-01, dB= 1.41000003e-01 fudgeQQ = 0.5
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