<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><div>hi gmx-users</div><div><br></div><div>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 </div><div><br></div><div>; VARIOUS PREPROCESSING OPTIONS</div><div>title = Yo</div><div>cpp = /usr/bin/cpp</div><div>include = </div><div>define = </div><div><br></div><div>; RUN CONTROL PARAMETERS</div><div>integrator = md</div><div>; Start time
and timestep in ps</div><div>tinit = 0</div><div>dt = 0.001</div><div>nsteps = 500000</div><div>; For exact run continuation or redoing part of a run</div><div>init_step = 0</div><div>; mode for center of mass motion removal</div><div>comm-mode = Linear</div><div>; number of steps for center of mass motion removal</div><div>nstcomm = 1</div><div>; group(s) for center of mass motion removal</div><div>comm-grps = </div><div><br></div><div>; ENERGY MINIMIZATION OPTIONS</div><div>; Force tolerance and initial
step-size</div><div>emtol = 10</div><div>emstep = 0.01</div><div>; Max number of iterations in relax_shells</div><div>niter = 20</div><div>; Step size (1/ps^2) for minimization of flexible constraints</div><div>fcstep = 0</div><div>; Frequency of steepest descents steps when doing CG</div><div>nstcgsteep = 1000</div><div>nbfgscorr = 10</div><div><br></div><div>; NEIGHBORSEARCHING PARAMETERS</div><div>; nblist update frequency</div><div>nstlist = 5</div><div>; ns algorithm (simple or grid)</div><div>ns_type
= grid</div><div>; Periodic boundary conditions: xyz (default), no (vacuum)</div><div>; or full (infinite systems only)</div><div>pbc = xyz</div><div>; nblist cut-off </div><div>rlist = 1.5</div><div>domain-decomposition = no</div><div><br></div><div>; OPTIONS FOR ELECTROSTATICS AND VDW</div><div>; Method for doing electrostatics</div><div>coulombtype = PME</div><div>rcoulomb-switch = 0</div><div>rcoulomb = 1.5</div><div>; Dielectric constant (DC) for cut-off or DC of reaction field</div><div>epsilon-r = 1</div><div>; Method for doing Van
der Waals</div><div>vdw-type = Cut-off</div><div>; cut-off lengths </div><div>rvdw-switch = 0</div><div>rvdw = 1.5</div><div>; Apply long range dispersion corrections for Energy and Pressure</div><div>DispCorr = EnerPres</div><div>; Extension of the potential lookup tables beyond the cut-off</div><div>table-extension = 1</div><div>; Spacing for the PME/PPPM FFT grid</div><div>fourierspacing = 0.12</div><div>; FFT grid size, when a value is 0 fourierspacing will be used</div><div>fourier_nx = 0</div><div>fourier_ny = 0</div><div>fourier_nz
= 0</div><div>; EWALD/PME/PPPM parameters</div><div>pme_order = 4</div><div>ewald_rtol = 1e-05</div><div>ewald_geometry = 3d</div><div>epsilon_surface = 0</div><div>optimize_fft = no</div><div><br></div><div>; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)</div><div>implicit_solvent = No</div><div><br></div><div>; OPTIONS FOR WEAK COUPLING ALGORITHMS</div><div>; Temperature coupling </div><div>Tcoupl = nose-hoover</div><div>; Groups to couple separately</div><div>tc-grps = System</div><div>; Time constant (ps) and
reference temperature (K)</div><div>tau_t = 0.1</div><div>ref_t = 298</div><div>; Pressure coupling </div><div>Pcoupl = Berendsen</div><div>Pcoupltype = isotropic</div><div>; Time constant (ps), compressibility (1/bar) and reference P (bar)</div><div>tau_p = 1</div><div>compressibility = 4.5e-5</div><div>ref_p = 1.0</div><div>; Random seed for Andersen thermostat</div><div>andersen_seed = 815131</div><div><br></div><div>; SIMULATED ANNEALING </div><div>; Type of annealing
for each temperature group (no/single/periodic)</div><div>annealing = no</div><div>; Number of time points to use for specifying annealing in each group</div><div>annealing_npoints = </div><div>; List of times at the annealing points for each group</div><div>annealing_time = </div><div>; Temp. at each annealing point, for each group.</div><div>annealing_temp = </div><div><br></div><div>; GENERATE VELOCITIES FOR STARTUP RUN</div><div>gen_vel = yes</div><div>gen_temp = 300</div><div>gen_seed = 1993</div><div><br></div><div>; OPTIONS FOR BONDS </div><div>constraints
= all-bonds</div><div>; Type of constraint algorithm</div><div>constraint-algorithm = Lincs</div><div>; Do not constrain the start configuration</div><div>unconstrained-start = no</div><div>; Use successive overrelaxation to reduce the number of shake iterations</div><div>Shake-SOR = no</div><div>; Relative tolerance of shake</div><div>shake-tol = 1e-04</div><div>; Highest order in the expansion of the constraint coupling matrix</div><div>lincs-order = 4 </div><div>; Number of iterations in the final step of LINCS. 1 is fine for</div><div>; normal simulations, but use 2 to conserve energy in NVE runs.</div><div>; For energy minimization with constraints it should be 4 to 8.</div><div>lincs-iter =
1</div><div>; Lincs will write a warning to the stderr if in one step a bond</div><div>; rotates over more degrees than</div><div>lincs-warnangle = 30</div><div>; Convert harmonic bonds to morse potentials</div><div>morse = no</div><div><br></div><div>; ENERGY GROUP EXCLUSIONS</div><div>; Pairs of energy groups for which all non-bonded interactions are excluded</div><div>energygrp_excl = </div><div><br></div><div><br></div><div><br></div><div>the top file is</div><div><br></div><div>[ defaults ]</div><div>; nbfunc<span class="Apple-tab-span" style="white-space:pre">        </span>comb-rule<span class="Apple-tab-span" style="white-space:pre">        </span>gen-pairs<span class="Apple-tab-span" style="white-space:pre">        </span>fudgeLJ<span class="Apple-tab-span" style="white-space:pre">        </span>fudgeQQ</div><div> 1<span
class="Apple-tab-span" style="white-space:pre">                </span>1<span class="Apple-tab-span" style="white-space:pre">                </span>no 0 0.5</div><div><br></div><div><br></div><div>[ atomtypes ]</div><div>; type mass charge ptype c6 c12</div><div> CH3 15.035 0.000 A 9.0638e-3 2.5206e-5</div><div> CH2 14.027 0.000 A 5.8108e-3 2.2071e-5</div><div> OS 15.999 0.000 A 8.8147e-4 4.2477e-7 </div><div> OA 15.999 0.000 A
2.3465e-3 1.7802e-6</div><div> HO 1.008 0.000 A 0.0000e00 0.0000e00 </div><div><br></div><div><br></div><div>[ moleculetype ]</div><div>; Name nrexcl</div><div>DRG 3</div><div><br></div><div>[ atoms ]</div><div>; nr type resnr resid atom cgnr charge mass</div><div> 1 CH3 1 DRG CAA 1 0.000 15.035</div><div> 2 CH2 1 DRG CAC 1 0.000 14.027</div><div> 3 CH2 1 DRG CAE 1 0.000 14.027</div><div>
4 CH2 1 DRG CAF 1 0.000 14.027</div><div> 5 CH2 1 DRG CAG 2 0.000 14.027</div><div> 6 CH2 1 DRG CAI 2 0.250 14.027</div><div> 7 OS 1 DRG OAM 2 -0.500 15.999</div><div> 8 CH2 1 DRG CAK 2 0.250 14.027</div><div> 9 CH2 1 DRG CAJ 3 0.250 14.027 </div><div> 10 OS 1 DRG
OAL 3 -0.500 15.999 </div><div> 11 CH2 1 DRG CAH 3 0.250 14.027 </div><div> 12 CH2 1 DRG CAD 4 0.265 14.027</div><div> 13 OA 1 DRG OAB 4 -0.700 15.999 </div><div> 14 HO 1 DRG HAA 4 0.435 1.008</div><div><br></div><div>[ bonds ]</div><div>; ai aj funct c0 c1</div><div>1 2<span class="Apple-tab-span" style="white-space:pre">        </span>1<span class="Apple-tab-span"
style="white-space:pre">        </span> 0.15400 517488.48</div><div>2 3<span class="Apple-tab-span" style="white-space:pre">        </span>1<span class="Apple-tab-span" style="white-space:pre">        </span> 0.15400 517488.48</div><div>3 4 1 0.15400 517488.48</div><div>4 5 1 0.15400 517488.48</div><div>5 6 1 0.15400 517488.48</div><div>6 7 1 0.14100 618809.04</div><div>7 8 1 0.14100 618809.04</div><div>8
9 1 0.15400 517488.48</div><div>9 10 1 0.14100 618809.04</div><div>10 11 1 0.14100 618809.04</div><div>11 12 1 0.15400 517488.48</div><div>12 13 1 0.14300 618809.04</div><div>13 14 1 0.09450 618809.04</div><div><br></div><div>[ angles ]</div><div>; ai aj ak funct c0 c1</div><div> 1 2 3
1 114.00 519.65</div><div> 2 3 4 1 114.00 519.65</div><div> 3 4 5 1 114.00 519.65</div><div> 4 5 6 1 114.00 519.65</div><div> 5 6 7 1 112.00 418.22</div><div> 6 7 8 1 112.00 502.19</div><div> 7 8 9 1 112.00 418.22</div><div> 8 9 10 1 112.00 418.22</div><div>
9 10 11 1 112.00 502.19</div><div> 10 11 12 1 112.00 418.22</div><div> 11 12 13 1 109.47 419.05</div><div> 12 13 14 1 108.50 460.62</div><div><br></div><div>[ pairs ]</div><div>; ai aj funct </div><div> 1 4 1 0 0 0 0</div><div> 2 5 1 0 0 0 0</div><div> 3 6 1 0 0 0 0</div><div> 4 7 1 0 0 0 0</div><div> 5 8 1 0 0 0 0</div><div> 6 9 1 0 0 0 0</div><div> 7 10 1 0 0 0 0</div><div> 8 11 1 0 0 0 0</div><div> 9 12 1 0 0 0 0</div><div>10 13 1 0 0 0
0</div><div>11 14 1 0 0 0 0</div><div>;</div><div>10 14 2 0 0 0 0 3.325789e-7</div><div><br></div><div><br></div><div>[ dihedrals ]</div><div>; ai aj ak al funct c0 c1 c2 c3 c4 c5</div><div> 1 2 3 4 3 8.231078 16.952626 1.133928 -26.317632 0.000000e+00 0.000000e+00</div><div> 2 3 4 5 3 8.231078 16.952626 1.133928 -26.317632 0.000000e+00 0.000000e+00</div><div> 3 4 5 6 3 8.231078 16.952626 1.133928 -26.317632 0.000000e+00 0.000000e+00</div><div> 4 5 6 7 3 6.983076 17.736182 0.886988 -25.606246 0.000000e+00 0.000000e+00</div><div> 5 6 7
8 3 7.949051 7.892513 2.722990 -18.564553 0.000000e+00 0.000000e+00</div><div> 6 7 8 9 3 7.949051 7.892513 2.722990 -18.564553 0.000000e+00 0.000000e+00</div><div> 7 8 9 10 3 8.368267 25.104800 4.184175 -33.473067 0.000000e+00 0.000000e+00</div><div> 8 9 10 11 3 7.949051 7.892513 2.722990 -18.564553 0.000000e+00 0.000000e+00</div><div> 9 10 11 12 3 7.949051 7.892513 2.722990 -18.564553 0.000000e+00 0.000000e+00</div><div> 10 11 12 13 3 8.368267 25.104800 4.184175 -33.473067 0.000000e+00 0.000000e+00</div><div> 11 12 13 14 3 2.822015 2.943074 0.485066 -6.250155 0.000000e+00 0.000000e+00</div><div><br></div><div>[ system ]</div><div>ciej </div><div><br></div><div>[ molecules
]</div><div>DRG<span class="Apple-tab-span" style="white-space:pre">        </span> 1</div><div><br></div><div>and the gro file is</div><div><br></div><div>PRODRG COORDS</div><div> 14</div><div> 1DRG CAA 1 0.313 0.879 0.001</div><div> 1DRG CAC 2 0.381 0.742 0.002</div><div> 1DRG CAE 3 0.534 0.757 0.000</div><div> 1DRG CAF 4 0.601 0.620 0.001</div><div> 1DRG CAG 5 0.754 0.634 -0.001</div><div> 1DRG CAI 6 0.821 0.497 0.001</div><div> 1DRG OAM 7 0.964 0.513 -0.001</div><div> 1DRG CAK
8 1.026 0.383 0.001</div><div> 1DRG CAJ 9 1.177 0.399 -0.001</div><div> 1DRG OAL 10 1.238 0.268 0.001</div><div> 1DRG CAH 11 1.382 0.282 0.000</div><div> 1DRG CAD 12 1.446 0.143 0.002</div><div> 1DRG OAB 13 1.588 0.156 0.001</div><div> 1DRG HAA 14 1.630 0.066 0.002</div><div> 4.00000 4.00000 4.00000</div><div><br></div><div>as you can see at top file there is a line in pairs which syntaxis is</div><div><br></div><div>10 14 2 0 0 0 0 3.325789e-7</div><div><br></div><div>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. </div><div><br></div><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></td></tr></table><br>