<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><div>i did three simulations</div><div><br></div><div>1) leaving the top file as it is above</div><div>2) deleting the [pairs] and all the lines below</div><div>3) deleting only the last line of the [pairs]</div><div><br></div><div>the results with usage of the command gmxdump -s topol.tpr | less</div><div>for step 0 are below</div><div><br></div><div>1)leaving the top file as it is above</div><div><br></div><div>I)from md.log</div><div><br></div><div>Step Time Lambda</div><div> 0 0.00000 0.00000</div><div><br></div><div>Grid: 3 x 3 x 3 cells</div><div>Long Range LJ corr.: <C6> 3.8522e-03</div><div>Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir:
0.00732091</div><div> Energies (kJ/mol)</div><div> Angle Ryckaert-Bell. LJ-14 Coulomb-14 LJ (SR)</div><div> 5.70628e+00 8.37083e+00 6.80805e-03 1.72679e+02 -3.25801e+00</div><div> Disper. corr. Coulomb (SR) Coul. recip. Potential Kinetic En.</div><div> -7.32091e-03 -2.93587e+01 -1.21273e+02 3.28661e+01 3.94838e+01</div><div> Total Energy Temperature Pressure (bar) Cons. rmsd ()</div><div> 7.23499e+01 3.65291e+02 4.25495e+01 3.43881e-07</div><div><br></div><div>II) from gmxdump</div><div><br></div><div>ffparams:</div><div>
atnr=5</div><div> ntypes=41</div><div> functype[0]=LJ_SR, c6= 9.06379987e-03, c12= 2.52059999e-05</div><div> functype[1]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05</div><div> functype[2]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06</div><div> functype[3]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06</div><div> functype[4]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[5]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05</div><div> functype[6]=LJ_SR, c6= 5.81080001e-03, c12= 2.20710008e-05</div><div> functype[7]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06</div><div> functype[8]=LJ_SR, c6= 3.69256595e-03,
c12= 6.26823703e-06</div><div> functype[9]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[10]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06</div><div> functype[11]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06</div><div> functype[12]=LJ_SR, c6= 8.81469983e-04, c12= 4.24770008e-07</div><div> functype[13]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07</div><div> functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[15]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06</div><div> functype[16]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06</div><div> functype[17]=LJ_SR, c6= 1.43818266e-03, c12=
8.69583573e-07</div><div> functype[18]=LJ_SR, c6= 2.34650006e-03, c12= 1.78020002e-06</div><div> functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[20]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[22]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[23]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[24]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[25]=ANGLES, thA= 1.14000e+02, ctA= 5.19650e+02, thB= 1.14000e+02, ctB= 5.19650e+02</div><div> functype[26]=ANGLES, thA= 1.12000e+02, ctA=
4.18220e+02, thB= 1.12000e+02, ctB= 4.18220e+02</div><div> functype[27]=ANGLES, thA= 1.12000e+02, ctA= 5.02190e+02, thB= 1.12000e+02, ctB= 5.02190e+02</div><div> functype[28]=ANGLES, thA= 1.09470e+02, ctA= 4.19050e+02, thB= 1.09470e+02, ctB= 4.19050e+02</div><div> functype[29]=ANGLES, thA= 1.08500e+02, ctA= 4.60620e+02, thB= 1.08500e+02, ctB= 4.60620e+02</div><div> 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</div><div>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</div><div> 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</div><div>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</div><div> 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</div><div>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</div><div> 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</div><div>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</div><div> 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</div><div>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</div><div> functype[35]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00</div><div> functype[36]=LJC14_Q, fqq= 0.00000000e+00, qi= 0.00000000e+00, qj= 0.00000000e+00, c6= 0.00000000e+00, c12= 3.32578907e-07</div><div> functype[37]=CONSTR, dA= 1.53999999e-01, dB= 1.53999999e-01</div><div> functype[38]=CONSTR, dA= 9.44999978e-02, dB= 9.44999978e-02</div><div>
functype[39]=CONSTR, dA= 1.43000007e-01, dB= 1.43000007e-01</div><div> functype[40]=CONSTR, dA= 1.41000003e-01, dB= 1.41000003e-01</div><div> fudgeQQ = 0.5</div><div><br></div><div>2) deleting the [pairs] and all the lines below</div><div><br></div><div>I)from md.log</div><div><br></div><div>Step Time Lambda</div><div> 0 0.00000 0.00000</div><div><br></div><div>Grid: 3 x 3 x 3 cells</div><div>Long Range LJ corr.: <C6> 3.8522e-03</div><div>Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091</div><div> Energies (kJ/mol)</div><div> Angle Ryckaert-Bell. LJ (SR)
Disper. corr. Coulomb (SR)</div><div> 5.70628e+00 8.37083e+00 -3.25801e+00 -7.32091e-03 -2.93587e+01</div><div> Coul. recip. Potential Kinetic En. Total Energy Temperature</div><div> -1.21273e+02 -1.39819e+02 3.94033e+01 -1.00416e+02 3.64546e+02</div><div> Pressure (bar) Cons. rmsd ()</div><div> 3.09781e+01 3.89303e-07</div><div><br></div><div>II) from gmxdump</div><div><br></div><div>ffparams:</div><div> atnr=5</div><div> ntypes=39</div><div> functype[0]=LJ_SR, c6= 9.06379987e-03, c12= 2.52059999e-05</div><div> functype[1]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05</div><div>
functype[2]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06</div><div> functype[3]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06</div><div> functype[4]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[5]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05</div><div> functype[6]=LJ_SR, c6= 5.81080001e-03, c12= 2.20710008e-05</div><div> functype[7]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06</div><div> functype[8]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06</div><div> functype[9]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[10]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06</div><div> functype[11]=LJ_SR, c6= 2.26319372e-03,
c12= 3.06187826e-06</div><div> functype[12]=LJ_SR, c6= 8.81469983e-04, c12= 4.24770008e-07</div><div> functype[13]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07</div><div> functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[15]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06</div><div> functype[16]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06</div><div> functype[17]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07</div><div> functype[18]=LJ_SR, c6= 2.34650006e-03, c12= 1.78020002e-06</div><div> functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[20]=LJ_SR, c6= 0.00000000e+00, c12=
0.00000000e+00</div><div> functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[22]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[23]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[24]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div>functype[25]=ANGLES, thA= 1.14000e+02, ctA= 5.19650e+02, thB= 1.14000e+02, ctB= 5.19650e+02</div><div> functype[26]=ANGLES, thA= 1.12000e+02, ctA= 4.18220e+02, thB= 1.12000e+02, ctB= 4.18220e+02</div><div> functype[27]=ANGLES, thA= 1.12000e+02, ctA= 5.02190e+02, thB= 1.12000e+02, ctB= 5.02190e+02</div><div> functype[28]=ANGLES, thA= 1.09470e+02, ctA= 4.19050e+02, thB= 1.09470e+02, ctB= 4.19050e+02</div><div>
functype[29]=ANGLES, thA= 1.08500e+02, ctA= 4.60620e+02, thB= 1.08500e+02, ctB= 4.60620e+02</div><div> 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</div><div>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</div><div> 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</div><div>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</div><div> 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</div><div>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</div><div> 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</div><div>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</div><div> 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</div><div>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</div><div> functype[35]=CONSTR, dA= 1.53999999e-01, dB= 1.53999999e-01</div><div> functype[36]=CONSTR, dA= 9.44999978e-02, dB= 9.44999978e-02</div><div> functype[37]=CONSTR, dA= 1.43000007e-01, dB= 1.43000007e-01</div><div> functype[38]=CONSTR, dA= 1.41000003e-01, dB= 1.41000003e-01</div><div> fudgeQQ = 0.5</div><div><br></div><div>3) deleting only the last line of the [pairs]</div><div><br></div><div>I)from md.log</div><div><br></div><div>Step Time Lambda</div><div> 0 0.00000
0.00000</div><div><br></div><div>Grid: 3 x 3 x 3 cells</div><div>Long Range LJ corr.: <C6> 3.8522e-03</div><div>Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091</div><div> Energies (kJ/mol)</div><div> Angle Ryckaert-Bell. LJ-14 Coulomb-14 LJ (SR)</div><div> 5.70628e+00 8.37083e+00 0.00000e+00 1.72679e+02 -3.25801e+00</div><div> Disper. corr. Coulomb (SR) Coul. recip. Potential Kinetic En.</div><div> -7.32091e-03 -2.93587e+01 -1.21273e+02 3.28593e+01 3.94837e+01</div><div> Total Energy Temperature Pressure (bar) Cons. rmsd ()</div><div> 7.23430e+01 3.65290e+02
4.25425e+01 3.43881e-07</div><div><br></div><div>II) from gmxdump</div><div><br></div><div>ffparams:</div><div> atnr=5</div><div> ntypes=40</div><div> functype[0]=LJ_SR, c6= 9.06379987e-03, c12= 2.52059999e-05</div><div> functype[1]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05</div><div> functype[2]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06</div><div> functype[3]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06</div><div> functype[4]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[5]=LJ_SR, c6= 7.25726737e-03, c12= 2.35864718e-05</div><div> functype[6]=LJ_SR, c6= 5.81080001e-03, c12= 2.20710008e-05</div><div>
functype[7]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06</div><div> functype[8]=LJ_SR, c6= 3.69256595e-03, c12= 6.26823703e-06</div><div> functype[9]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[10]=LJ_SR, c6= 2.82656471e-03, c12= 3.27211751e-06</div><div> functype[11]=LJ_SR, c6= 2.26319372e-03, c12= 3.06187826e-06</div><div> functype[12]=LJ_SR, c6= 8.81469983e-04, c12= 4.24770008e-07</div><div> functype[13]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07</div><div> functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[15]=LJ_SR, c6= 4.61174641e-03, c12= 6.69863584e-06</div><div> functype[16]=LJ_SR,
c6= 3.69256595e-03, c12= 6.26823703e-06</div><div> functype[17]=LJ_SR, c6= 1.43818266e-03, c12= 8.69583573e-07</div><div> functype[18]=LJ_SR, c6= 2.34650006e-03, c12= 1.78020002e-06</div><div> functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[20]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[22]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[23]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[24]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00</div><div> functype[25]=ANGLES, thA= 1.14000e+02, ctA=
5.19650e+02, thB= 1.14000e+02, ctB= 5.19650e+02</div><div> functype[26]=ANGLES, thA= 1.12000e+02, ctA= 4.18220e+02, thB= 1.12000e+02, ctB= 4.18220e+02</div><div> functype[27]=ANGLES, thA= 1.12000e+02, ctA= 5.02190e+02, thB= 1.12000e+02, ctB= 5.02190e+02</div><div> functype[28]=ANGLES, thA= 1.09470e+02, ctA= 4.19050e+02, thB= 1.09470e+02, ctB= 4.19050e+02</div><div> functype[29]=ANGLES, thA= 1.08500e+02, ctA= 4.60620e+02, thB= 1.08500e+02, ctB= 4.60620e+02</div><div> 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</div><div>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</div><div> 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</div><div>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</div><div> 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</div><div>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</div><div> 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</div><div>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</div><div> 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</div><div>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</div><div> functype[35]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00</div><div> functype[36]=CONSTR, dA= 1.53999999e-01, dB= 1.53999999e-01</div><div> functype[37]=CONSTR, dA= 9.44999978e-02, dB= 9.44999978e-02</div><div> functype[38]=CONSTR,
dA= 1.43000007e-01, dB= 1.43000007e-01</div><div> functype[39]=CONSTR, dA= 1.41000003e-01, dB= 1.41000003e-01</div><div> fudgeQQ = 0.5</div><div><br></div><div><br></div><div>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.</div><div><br></div><div>Please </div><div><br></div><div>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.</div><div> i think it is is smth simple that i miss here and i call your experience on this problem.</div><div>if you want more details i will do whatever i can to give it to you.</div><div><br></div><div>thank you </div></td></tr></table><br>