[gmx-users] Re: Energy miscalculation

Thanasis Koukoulas koukoulas_th at yahoo.gr
Mon Jun 21 13:13:10 CEST 2010

3) deleting only the last line of the [pairs]
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-14     Coulomb-14        LJ (SR)    5.70628e+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    4.25425e+01    3.43881e-07
II) from gmxdump
ffparams:      atnr=5      ntypes=40         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+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]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00         functype[36]=CONSTR, dA= 1.53999999e-01, dB= 1.53999999e-01         functype[37]=CONSTR, dA= 9.44999978e-02, dB= 9.44999978e-02         functype[38]=CONSTR, dA= 1.43000007e-01, dB= 1.43000007e-01         functype[39]=CONSTR, dA= 1.41000003e-01, dB= 1.41000003e-01      fudgeQQ              = 0.5

I have several reasons to believe that gromacs dont give the right results although it "understands" the values of my input top file. the model i use is Trappe and my colleague researcher which use the exact model of this molecule finds different results from mine. the fact that the  results from my fellow colleague are accepted as standards in this lab plus the positive total energy of mine  and abnormal value of density (0.96 gr/ml) i take from my results brought me to the conclusion that smth is wrong in gromacs.
knowing that this isnt your concern and you offer your help without effort encourage me to continue to this project and understand the way that gromacs works. believe me that i have been working hard on this and these are not words of someone lazy who wants the work to be done by smone else. i think it is is smth simple that i miss here and  i call your experience on this problem.if you want more details i will do whatever i can to give it to you.
thank you 

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