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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">Respected Sir,</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">Myself Haresh<span style="mso-spacerun: yes"> </span>Ajani from National Institute of Pharmaceutical Education & Research.</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">I am using gromacs version 4.5.3. I am working on molded Protein.</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">I am facing one problem in gromacs after minimization of the protein.</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">I have put my query here.</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">Fatal Error : Wrote pdb files with previous and current coordinates</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">Warning: 1-4 interaction between 687 and 691 at distance 4.001 which is larger than the 1-4 table size 2.000 nm</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">These are ignored for the rest of the simulation</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">This usually means your system is exploding,</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">if not, you should increase table-extension in your mdp file</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">or with user tables increase the table size</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">Fatal error:</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">9 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">This usually means that your system is not well equilibrated.</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">I have given run for gromacs.</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">Pdb2gmx -f 1.pdb -o 12.pdb -p 12.top -ignh -ter -missing</font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">then I have selected gromos force field and SPC water model.</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">editconf -bt cubic -f 12.pdb -o 123.pdb -c -d 0.9</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">genbox -cp 123.pdb -cs spc216.gro -p 123.top -o 123_b4ion.pdb </font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>then neutralize the protein and<span style="mso-spacerun: yes"> </span>energy minimization.</font></font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">Steepest Descents:</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>Tolerance (Fmax)<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>1.00000e+03</font></font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>Number of steps<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>3500</font></font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">writing lowest energy coordinates.</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">Steepest Descents converged to Fmax < 1000 in 3468 steps</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">Potential Energy<span style="mso-spacerun: yes"> </span>= -9.6223600e+05</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">Maximum force<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>9.3264703e+02 on atom 695</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">Norm of force<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>2.5498827e+01</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">Step 0, time 0 (ps)<span style="mso-spacerun: yes"> </span>LINCS WARNING</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">relative constraint deviation after LINCS:</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">rms 0.003107, max 0.020384 (between atoms 642 and 643)</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">bonds that rotated more than 30 degrees:</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>atom 1 atom 2<span style="mso-spacerun: yes"> </span>angle<span style="mso-spacerun: yes"> </span>previous, current, constraint length</font></font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">starting mdrun 'MD_loweng_model1 in water'</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">12500 steps,<span style="mso-spacerun: yes"> </span>25.0 ps.</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">Step 0, time 0 (ps)<span style="mso-spacerun: yes"> </span>LINCS WARNING</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">relative constraint deviation after LINCS:</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">rms 18.316392, max 238.458267 (between atoms 695 and 696)</font></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">bonds that rotated more than 30 degrees:</font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>atom 1 atom 2<span style="mso-spacerun: yes"> </span>angle<span style="mso-spacerun: yes"> </span>previous, current, constraint length</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>685<span style="mso-spacerun: yes"> </span>686<span style="mso-spacerun: yes"> </span>30.9<span style="mso-spacerun: yes"> </span><span style="mso-spacerun: yes"> </span>0.1530<span style="mso-spacerun: yes"> </span>0.1317<span style="mso-spacerun: yes"> </span>0.1530</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>686<span style="mso-spacerun: yes"> </span>687<span style="mso-spacerun: yes"> </span>60.3<span style="mso-spacerun: yes"> </span>0.1531<span style="mso-spacerun: yes"> </span>0.2200<span style="mso-spacerun: yes"> </span>0.1530</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>687<span style="mso-spacerun: yes"> </span>688<span style="mso-spacerun: yes"> </span>64.2<span style="mso-spacerun: yes"> </span>0.1534<span style="mso-spacerun: yes"> </span>1.3927<span style="mso-spacerun: yes"> </span>0.1530</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>629<span style="mso-spacerun: yes"> </span>631<span style="mso-spacerun: yes"> </span>62.2<span style="mso-spacerun: yes"> </span>0.1332<span style="mso-spacerun: yes"> </span>0.2212<span style="mso-spacerun: yes"> </span>0.1330</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>629<span style="mso-spacerun: yes"> </span>630<span style="mso-spacerun: yes"> </span>32.4<span style="mso-spacerun: yes"> </span>0.1231<span style="mso-spacerun: yes"> </span>0.1531<span style="mso-spacerun: yes"> </span>0.1230</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>631<span style="mso-spacerun: yes"> </span><span style="mso-spacerun: yes"> </span>633<span style="mso-spacerun: yes"> </span>80.2<span style="mso-spacerun: yes"> </span>0.1476<span style="mso-spacerun: yes"> </span>1.2395<span style="mso-spacerun: yes"> </span>0.1470</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>631<span style="mso-spacerun: yes"> </span>632<span style="mso-spacerun: yes"> </span>73.3<span style="mso-spacerun: yes"> </span>0.1001<span style="mso-spacerun: yes"> </span>0.1563<span style="mso-spacerun: yes"> </span>0.1000</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>633<span style="mso-spacerun: yes"> </span>650<span style="mso-spacerun: yes"> </span>64.8<span style="mso-spacerun: yes"> </span>0.1536<span style="mso-spacerun: yes"> </span>1.1461<span style="mso-spacerun: yes"> </span>0.1530</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>633<span style="mso-spacerun: yes"> </span>634<span style="mso-spacerun: yes"> </span>84.1<span style="mso-spacerun: yes"> </span>0.1561<span style="mso-spacerun: yes"> </span>2.3556<span style="mso-spacerun: yes"> </span>0.1530</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>634<span style="mso-spacerun: yes"> </span>635<span style="mso-spacerun: yes"> </span>38.9<span style="mso-spacerun: yes"> </span>0.1557<span style="mso-spacerun: yes"> </span>6.0052<span style="mso-spacerun: yes"> </span>0.1530</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>635<span style="mso-spacerun: yes"> </span>638<span style="mso-spacerun: yes"> </span>85.4<span style="mso-spacerun: yes"> </span>0.1413<span style="mso-spacerun: yes"> </span>6.8134<span style="mso-spacerun: yes"> </span>0.1390</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>635<span style="mso-spacerun: yes"> </span>636<span style="mso-spacerun: yes"> </span>90.6<span style="mso-spacerun: yes"> </span>0.1344<span style="mso-spacerun: yes"> </span>12.6580<span style="mso-spacerun: yes"> </span>0.1330</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>636<span style="mso-spacerun: yes"> </span>639<span style="mso-spacerun: yes"> </span>37.3<span style="mso-spacerun: yes"> </span>0.1336<span style="mso-spacerun: yes"> </span>7.0188<span style="mso-spacerun: yes"> </span>0.1330</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>636<span style="mso-spacerun: yes"> </span>637<span style="mso-spacerun: yes"> </span>149.3<span style="mso-spacerun: yes"> </span>0.1099<span style="mso-spacerun: yes"> </span>8.2681<span style="mso-spacerun: yes"> </span>0.1090</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>638<span style="mso-spacerun: yes"> </span>642<span style="mso-spacerun: yes"> </span>54.8<span style="mso-spacerun: yes"> </span>0.1404<span style="mso-spacerun: yes"> </span>1.8808<span style="mso-spacerun: yes"> </span>0.1390</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>638<span style="mso-spacerun: yes"> </span>641<span style="mso-spacerun: yes"> </span>70.5<span style="mso-spacerun: yes"> </span>0.1405<span style="mso-spacerun: yes"> </span>1.9874<span style="mso-spacerun: yes"> </span>0.1390</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>639<span style="mso-spacerun: yes"> </span>641<span style="mso-spacerun: yes"> </span>119.2<span style="mso-spacerun: yes"> </span>0.1342<span style="mso-spacerun: yes"> </span>5.2357<span style="mso-spacerun: yes"> </span>0.1330</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>639<span style="mso-spacerun: yes"> </span>640<span style="mso-spacerun: yes"> </span>118.9<span style="mso-spacerun: yes"> </span>0.1009<span style="mso-spacerun: yes"> </span>3.3865<span style="mso-spacerun: yes"> </span>0.1000</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>641<span style="mso-spacerun: yes"> </span>644<span style="mso-spacerun: yes"> </span>68.6<span style="mso-spacerun: yes"> </span>0.1402<span style="mso-spacerun: yes"> </span>1.9737<span style="mso-spacerun: yes"> </span>0.1390</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>642<span style="mso-spacerun: yes"> </span>646<span style="mso-spacerun: yes"> </span>68.7 <span style="mso-spacerun: yes"> </span>0.1417<span style="mso-spacerun: yes"> </span>0.2159<span style="mso-spacerun: yes"> </span>0.1390</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>642<span style="mso-spacerun: yes"> </span>643<span style="mso-spacerun: yes"> </span>54.0<span style="mso-spacerun: yes"> </span>0.1112<span style="mso-spacerun: yes"> </span>0.1584<span style="mso-spacerun: yes"> </span>0.1090</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>644<span style="mso-spacerun: yes"> </span>648<span style="mso-spacerun: yes"> </span>81.7<span style="mso-spacerun: yes"> </span>0.1406<span style="mso-spacerun: yes"> </span>1.3960<span style="mso-spacerun: yes"> </span>0.1390</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>644<span style="mso-spacerun: yes"> </span>645<span style="mso-spacerun: yes"> </span>72.1<span style="mso-spacerun: yes"> </span>0.1103<span style="mso-spacerun: yes"> </span>0.8079<span style="mso-spacerun: yes"> </span>0.1090</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>646<span style="mso-spacerun: yes"> </span>648<span style="mso-spacerun: yes"> </span>65.5<span style="mso-spacerun: yes"> </span>0.1398<span style="mso-spacerun: yes"> </span>0.5901<span style="mso-spacerun: yes"> </span>0.1390</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>648 <span style="mso-spacerun: yes"> </span>649<span style="mso-spacerun: yes"> </span>67.1<span style="mso-spacerun: yes"> </span>0.1096<span style="mso-spacerun: yes"> </span>0.4282<span style="mso-spacerun: yes"> </span>0.1090</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>688<span style="mso-spacerun: yes"> </span>689<span style="mso-spacerun: yes"> </span>132.4<span style="mso-spacerun: yes"> </span>0.1490<span style="mso-spacerun: yes"> </span>1.4233<span style="mso-spacerun: yes"> </span>0.1470</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>689<span style="mso-spacerun: yes"> </span>690<span style="mso-spacerun: yes"> </span>151.7<span style="mso-spacerun: yes"> </span>0.1012<span style="mso-spacerun: yes"> </span>0.7597<span style="mso-spacerun: yes"> </span>0.1000</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>691<span style="mso-spacerun: yes"> </span>695<span style="mso-spacerun: yes"> </span>78.6<span style="mso-spacerun: yes"> </span>0.1357<span style="mso-spacerun: yes"> </span>22.8056<span style="mso-spacerun: yes"> </span>0.1340</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>691<span style="mso-spacerun: yes"> </span>692<span style="mso-spacerun: yes"> </span>57.4<span style="mso-spacerun: yes"> </span>0.1327<span style="mso-spacerun: yes"> </span>3.6809<span style="mso-spacerun: yes"> </span>0.1340</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>692<span style="mso-spacerun: yes"> </span>694<span style="mso-spacerun: yes"> </span>151.9<span style="mso-spacerun: yes"> </span>0.1014<span style="mso-spacerun: yes"> </span>0.5744<span style="mso-spacerun: yes"> </span>0.1000</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>692<span style="mso-spacerun: yes"> </span>693<span style="mso-spacerun: yes"> </span>165.2<span style="mso-spacerun: yes"> </span>0.1014<span style="mso-spacerun: yes"> </span>0.7382<span style="mso-spacerun: yes"> </span>0.1000</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>695<span style="mso-spacerun: yes"> </span>697<span style="mso-spacerun: yes"> </span>119.6<span style="mso-spacerun: yes"> </span>0.1012<span style="mso-spacerun: yes"> </span>18.8779<span style="mso-spacerun: yes"> </span>0.1000</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>695<span style="mso-spacerun: yes"> </span>696<span style="mso-spacerun: yes"> </span>86.1<span style="mso-spacerun: yes"> </span>0.1012<span style="mso-spacerun: yes"> </span>23.9458<span style="mso-spacerun: yes"> </span>0.1000</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>652<span style="mso-spacerun: yes"> </span>654<span style="mso-spacerun: yes"> </span>42.0<span style="mso-spacerun: yes"> </span>0.1471<span style="mso-spacerun: yes"> </span>0.2030<span style="mso-spacerun: yes"> </span>0.1470</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>652<span style="mso-spacerun: yes"> </span>653<span style="mso-spacerun: yes"> </span>50.7<span style="mso-spacerun: yes"> </span>0.1001<span style="mso-spacerun: yes"> </span>0.1549<span style="mso-spacerun: yes"> </span>0.1000</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>650<span style="mso-spacerun: yes"> </span>652<span style="mso-spacerun: yes"> </span>72.6<span style="mso-spacerun: yes"> </span>0.1333<span style="mso-spacerun: yes"> </span>0.2537<span style="mso-spacerun: yes"> </span>0.1330</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>650<span style="mso-spacerun: yes"> </span>651<span style="mso-spacerun: yes"> </span>69.2<span style="mso-spacerun: yes"> </span>0.1232<span style="mso-spacerun: yes"> </span>0.1942<span style="mso-spacerun: yes"> </span>0.1230</font></font><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">Wrote pdb files with previous and current coordinates</font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">Warning: 1-4 interaction between 687 and 691 at distance 4.001 which is larger than the 1-4 table size 2.000 nm</font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">These are ignored for the rest of the simulation</font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">This usually means your system is exploding,</font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">if not, you should increase table-extension in your mdp file</font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">or with user tables increase the table size</font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">Fatal error:</font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">9 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.</font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">This usually means that your system is not well equilibrated.</font></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3"> </font></p><br clear="all"><br>-- <br>Haresh Ajani<br>09925522578<br><br>