hi gmx-users In order to discover the miscalculation that gromacs computes in a system of 450 molecules in vacuum and after a gmx-user guidance i ran a simulation of one molecule in vacuum just to calculate by hand all the energies. the mdp file that i use is ; VARIOUS PREPROCESSING OPTIONS title = Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.001 nsteps = 500000 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed ;bd-temp = 300 bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol = 10 emstep = 0.01 ; Max number of iterations in relax_shells niter = 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr = 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 50 nstenergy = 50 ; Output frequency and precision for xtc file nstxtcout = 100 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 1.5 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.5 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.5 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = nose-hoover ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 0.1 ref_t = 298 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 ; Random seed for Andersen thermostat andersen_seed = 815131 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing = no ; Number of time points to use for specifying annealing in each group annealing_npoints = ; List of times at the annealing points for each group annealing_time = ; Temp. at each annealing point, for each group. annealing_temp = ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 300 gen_seed = 1993 ; OPTIONS FOR BONDS constraints = all-bonds ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration unconstrained-start = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake-tol = 1e-04 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 4 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. lincs-iter = 1 ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 30 ; Convert harmonic bonds to morse potentials morse = no ; ENERGY GROUP EXCLUSIONS ; Pairs of energy groups for which all non-bonded interactions are excluded energygrp_excl = the top file is [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 0 0.5 [ atomtypes ] ; type mass charge ptype c6 c12 CH3 15.035 0.000 A 9.0638e-3 2.5206e-5 CH2 14.027 0.000 A 5.8108e-3 2.2071e-5 OS 15.999 0.000 A 8.8147e-4 4.2477e-7 OA 15.999 0.000 A 2.3465e-3 1.7802e-6 HO 1.008 0.000 A 0.0000e00 0.0000e00 [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 DRG CAA 1 0.000 15.035 2 CH2 1 DRG CAC 1 0.000 14.027 3 CH2 1 DRG CAE 1 0.000 14.027 4 CH2 1 DRG CAF 1 0.000 14.027 5 CH2 1 DRG CAG 2 0.000 14.027 6 CH2 1 DRG CAI 2 0.250 14.027 7 OS 1 DRG OAM 2 -0.500 15.999 8 CH2 1 DRG CAK 2 0.250 14.027 9 CH2 1 DRG CAJ 3 0.250 14.027 10 OS 1 DRG OAL 3 -0.500 15.999 11 CH2 1 DRG CAH 3 0.250 14.027 12 CH2 1 DRG CAD 4 0.265 14.027 13 OA 1 DRG OAB 4 -0.700 15.999 14 HO 1 DRG HAA 4 0.435 1.008 [ bonds ] ; ai aj funct c0 c1 1 2 1 0.15400 517488.48 2 3 1 0.15400 517488.48 3 4 1 0.15400 517488.48 4 5 1 0.15400 517488.48 5 6 1 0.15400 517488.48 6 7 1 0.14100 618809.04 7 8 1 0.14100 618809.04 8 9 1 0.15400 517488.48 9 10 1 0.14100 618809.04 10 11 1 0.14100 618809.04 11 12 1 0.15400 517488.48 12 13 1 0.14300 618809.04 13 14 1 0.09450 618809.04 [ angles ] ; ai aj ak funct c0 c1 1 2 3 1 114.00 519.65 2 3 4 1 114.00 519.65 3 4 5 1 114.00 519.65 4 5 6 1 114.00 519.65 5 6 7 1 112.00 418.22 6 7 8 1 112.00 502.19 7 8 9 1 112.00 418.22 8 9 10 1 112.00 418.22 9 10 11 1 112.00 502.19 10 11 12 1 112.00 418.22 11 12 13 1 109.47 419.05 12 13 14 1 108.50 460.62 [ pairs ] ; ai aj funct 1 4 1 0 0 0 0 2 5 1 0 0 0 0 3 6 1 0 0 0 0 4 7 1 0 0 0 0 5 8 1 0 0 0 0 6 9 1 0 0 0 0 7 10 1 0 0 0 0 8 11 1 0 0 0 0 9 12 1 0 0 0 0 10 13 1 0 0 0 0 11 14 1 0 0 0 0 ; 10 14 2 0 0 0 0 3.325789e-7 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 1 2 3 4 3 8.231078 16.952626 1.133928 -26.317632 0.000000e+00 0.000000e+00 2 3 4 5 3 8.231078 16.952626 1.133928 -26.317632 0.000000e+00 0.000000e+00 3 4 5 6 3 8.231078 16.952626 1.133928 -26.317632 0.000000e+00 0.000000e+00 4 5 6 7 3 6.983076 17.736182 0.886988 -25.606246 0.000000e+00 0.000000e+00 5 6 7 8 3 7.949051 7.892513 2.722990 -18.564553 0.000000e+00 0.000000e+00 6 7 8 9 3 7.949051 7.892513 2.722990 -18.564553 0.000000e+00 0.000000e+00 7 8 9 10 3 8.368267 25.104800 4.184175 -33.473067 0.000000e+00 0.000000e+00 8 9 10 11 3 7.949051 7.892513 2.722990 -18.564553 0.000000e+00 0.000000e+00 9 10 11 12 3 7.949051 7.892513 2.722990 -18.564553 0.000000e+00 0.000000e+00 10 11 12 13 3 8.368267 25.104800 4.184175 -33.473067 0.000000e+00 0.000000e+00 11 12 13 14 3 2.822015 2.943074 0.485066 -6.250155 0.000000e+00 0.000000e+00 [ system ] ciej [ molecules ] DRG 1 and the gro file is PRODRG COORDS 14 1DRG CAA 1 0.313 0.879 0.001 1DRG CAC 2 0.381 0.742 0.002 1DRG CAE 3 0.534 0.757 0.000 1DRG CAF 4 0.601 0.620 0.001 1DRG CAG 5 0.754 0.634 -0.001 1DRG CAI 6 0.821 0.497 0.001 1DRG OAM 7 0.964 0.513 -0.001 1DRG CAK 8 1.026 0.383 0.001 1DRG CAJ 9 1.177 0.399 -0.001 1DRG OAL 10 1.238 0.268 0.001 1DRG CAH 11 1.382 0.282 0.000 1DRG CAD 12 1.446 0.143 0.002 1DRG OAB 13 1.588 0.156 0.001 1DRG HAA 14 1.630 0.066 0.002 4.00000 4.00000 4.00000 as you can see at top file there is a line in pairs which syntaxis is 10 14 2 0 0 0 0 3.325789e-7 it is an extra interaction that must be applied to the molecule according to the formula 3.325789e-7/r^12 the only way i could think importing this interaction as i have mentioned several times was the above. i did three simulations 1) leaving the top file as it is above 2) deleting the [pairs] and all the lines below 3) deleting only the last line of the [pairs] the results with usage of the command gmxdump -s topol.tpr | less for step 0 are below 1)leaving the top file as it is above I)from md.log Step Time Lambda 0 0.00000 0.00000 Grid: 3 x 3 x 3 cells Long Range LJ corr.: 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) 5.70628e+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 4.25495e+01 3.43881e-07 II) from gmxdump ffparams: atnr=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 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 cells Long Range LJ corr.: 3.8522e-03 Long 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+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]=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 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 cells Long Range LJ corr.: 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) 5.70628e+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+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]=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. Please 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