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<div>Hi</div>
<div>The follwing is my .out file.</div>
<div>From it, can I conclude that some molecule clashing with another ?</div>
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<div>Thank you</div>
<div>Lin</div>
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<div>Step -2, time -0.002 (ps) <strong>LINCS WARNING</strong><br>relative constraint deviation after LINCS:<br>max 0.044043 (between atoms 366 and 368) rms 0.001724<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br>
366 367 36.8 0.1973 0.1301 0.1250<br> 366 368 36.6 0.1963 0.1305 0.1250<br>starting mdrun 'HEN EGG WHITE LYSOZYME in water'<br>5000 steps, 5.0 ps.</div>
<div><br>Step 0, time 0 (ps) <strong>LINCS WARNING<br></strong>relative constraint deviation after LINCS:<br>max 42.623165 (between atoms 1499 and 1518) rms 2.341352<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br>
1376 1377 39.1 0.1470 0.1471 0.1470<br> 1404 1405 59.8 0.1430 0.2374 0.1430<br> 1405 1406 88.5 0.1530 0.2358 0.1530<br> 1406 1407 76.6 0.1530 0.1851 0.1530<br>
1407 1408 74.3 0.1531 0.2407 0.1530<br> 1438 1439 34.8 0.1530 0.1557 0.1530<br> 1439 1440 34.4 0.1530 0.1594 0.1530<br> 1499 1518 90.0 0.1090 4.7549 0.1090<br>
1554 1578 90.0 0.1090 0.2729 0.1090<br> 1594 1595 53.5 0.1390 0.1650 0.1390<br> 1595 1596 57.1 0.1390 0.1515 0.1390<br> 1595 1615 90.3 0.1090 0.5874 0.1090<br>
1666 1652 48.5 0.1392 0.1535 0.1390<br> 1654 1678 90.1 0.1092 0.4554 0.1090<br> 1656 1679 90.2 0.1092 0.1300 0.1090<br> 1657 1680 90.0 0.1092 1.6346 0.1090<br>
1660 1661 58.0 0.1393 0.1424 0.1390<br> 1661 1662 54.5 0.1392 0.1467 0.1390<br> 1661 1681 88.9 0.1091 0.1237 0.1090<br> 1665 1684 89.8 0.1091 0.3454 0.1090<br>
1667 1666 53.1 0.1531 0.1364 0.1530</div>
<div>Back Off! I just backed up step-1.pdb to ./#step-1.pdb.1#<br>Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2#</div>
<div>Back Off! I just backed up step-1.pdb to ./#step-1.pdb.1#</div>
<div>Back Off! I just backed up 6LYZ-PR.trr to ./#6LYZ-PR.trr.1#<br>Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2#<br>Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2#</div>
<div>Back Off! I just backed up step-1.pdb to ./#step-1.pdb.2#<br>Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2#</div>
<div>Back Off! I just backed up step-1.pdb to ./#step-1.pdb.2#<br>Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2#<br>Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2#</div>
<div>Step 0, time 0 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>max 597108032.000000 (between atoms 366 and 368) rms 26394490.000000<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br>
26 39 52.0 0.1530 0.1699 0.1530<br> 39 40 69.4 0.1230 0.1423 0.1230<br> 39 41 40.7 0.1330 0.1502 0.1330<br> 75 76 36.0 0.1250 0.1252 0.1250<br>
133 134 69.5 0.1530 0.1937 0.1530<br> 134 135 89.8 0.1470 0.2036 0.1470<br> 344 346 42.4 0.1470 0.2090 0.1470<br> 346 347 42.2 0.1530 0.2141 0.1530<br>
<font color="#ff0000"><strong> 346 359 63.9 0.1530 26006.0332 0.1530<br> 359 360 56.9 0.1230 26006.0469 0.1230<br> 359 361 83.2 0.1330 82898.5859 0.1330<br> 361 362 77.5 0.1000 82845.7109 0.1000<br>
361 363 83.8 0.1470 398710.1875 0.1470<br> 363 364 89.3 0.1530 1909291.8750 0.1530<br> 363 369 85.2 0.1530 393002.8125 0.1530<br> 364 365 90.0 0.1508 31146174.0000 0.1530<br>
365 366 90.2 0.1544 66925512.0000 0.1530<br> 366 367 92.7 0.1301 73689816.0000 0.1250<br> 366 368 87.0 0.1305 74638504.0000 0.1250<br> 369 370 72.1 0.1230 65978.3203 0.1230<br>
369 371 72.6 0.1330 66864.2812 0.1330<br> 371 372 85.7 0.1000 10685.0596 0.1000<br> 371 373 61.0 0.1470 10685.1035 0.1470<br></strong></font> 373 374 33.3 0.1530 0.1896 0.1530<br>
373 377 33.5 0.1530 0.1933 0.1530<br> 547 548 90.1 0.1089 0.1358 0.1090<br> 898 900 89.9 0.1530 0.4741 0.1530<br> 1045 1046 47.0 0.1780 0.1783 0.1780<br>
1118 1119 36.8 0.1090 0.1069 0.1090<br> 1128 1129 31.8 0.1000 0.1019 0.1000<br> 1130 1131 35.6 0.1340 0.1334 0.1340<br> 1152 1153 89.6 0.1530 0.2937 0.1530<br>
1153 1154 90.3 0.1529 2.2321 0.1530<br> 1154 1155 89.9 0.1529 7.7561 0.1530<br> 1155 1156 90.3 0.1470 8.2649 0.1470<br> 1156 1157 60.6 0.1000 0.1543 0.1000<br>
1156 1158 49.6 0.1339 0.1783 0.1340<br> 1158 1159 48.4 0.1340 0.1038 0.1340<br> 1159 1160 86.4 0.1000 0.1375 0.1000<br> 1165 1166 45.8 0.1230 0.1207 0.1230</div>
<div>Back Off! I just backed up step-1.pdb to ./#step-1.pdb.3#<br>Sorry couldn't backup step-1.pdb to ./#step-1.pdb.3#</div>
<div>Back Off! I just backed up step-1.pdb to ./#step-1.pdb.3#</div>
<div>Back Off! I just backed up step-1.pdb to ./#step-1.pdb.4#</div>
<div>Back Off! I just backed up step-1.pdb to ./#step-1.pdb.3#</div>
<div>Back Off! I just backed up step0.pdb to ./#step0.pdb.1#</div>
<div>Back Off! I just backed up step0.pdb to ./#step0.pdb.2#<br>Wrote pdb files with previous and current coordinates</div>
<div>Back Off! I just backed up step0.pdb to ./#step0.pdb.3#<br>Wrote pdb files with previous and current coordinates</div>
<div>Back Off! I just backed up step0.pdb to ./#step0.pdb.1#<br>Sorry couldn't backup step0.pdb to ./#step0.pdb.1#<br>Wrote pdb files with previous and current coordinates<br>Wrote pdb files with previous and current coordinates</div>
<div>Back Off! I just backed up step0.pdb to ./#step0.pdb.1#</div>
<div>Back Off! I just backed up step0.pdb to ./#step0.pdb.4#<br>Wrote pdb files with previous and current coordinates</div>
<div>Back Off! I just backed up step0.pdb to ./#step0.pdb.5#<br>Wrote pdb files with previous and current coordinates<br>Wrote pdb files with previous and current coordinates<br>Wrote pdb files with previous and current coordinates</div>
<div>Back Off! I just backed up step0.pdb to ./#step0.pdb.6#<br>Wrote pdb files with previous and current coordinates<br>Terminated<br></div>
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<div>Chih-Ying Lin wrote:<br>><br>><br>> Hi<br>> My simulation broke down and the simulation procedues are as follows.<br>><br>> 1. center a protein molecule in the simulation box<br>> 2. put 20 ligands around the protein with " genbox " command<br>
> 3. make sure that any atom of the ligands does not overlap on any atom<br>> of the protein with Visulization-software.<br>> 4. solvent addition , with the command " genbox *-vdwd* 0.2 "<br>> 5. Addition of ions, with the command " genion "<br>
> 6. Energy minimization of the solvated system<br>> 7. Position restrained MD<br>><br>> => simulation broke down.<br>> => It is very probable that some molecule clashing with another.</div>
<div>You can change "probable" to an actual answer if you analyze whatever LINCS<br>warnings are occurring (the atoms are listed) and by watching the resulting<br>trajectory.</div>
<div>> => since i have made sured that any atom of the ligands does not overlap<br>> on any atom of the protein with Visulization-software,<br>> the clashed pair of the molecules are possible " solvent vs<br>
> solvent " or "solvent vs protein" or "solvent vs<br>> ligand "</div>
<div>Then you should follow up #4 above with another visual inspection, as you did<br>with protein-ligand interactions, in addition to any information printed to the<br>log file (as above).</div>
<div>> => however, from the Gromacs manual , command "genbox"<br>> " Solvent molecules are removed from the box where the distance<br>> between any atom of the solute molecule(s) and any atom of the solvent<br>
> molecule is less<br>> than the sum of the VanderWaals radii of both atoms. A database<br>> (vdwradii.dat <<a href="http://manual.gromacs.org/current/online/dat.html">http://manual.gromacs.org/current/online/dat.html</a>>) of<br>
> VanderWaals radii is read by the program, atoms not in the<br>> database are assigned a default distance -vdw."<br>></div>
<div>So solvent-solvent overlap shouldn't be a problem.</div>
<div>> => here is vdwradii.dat (the ligand is simply made of C, N, O, H)</div>
<div>Yes, this is standard.</div>
<div>> ; Very approximate VanderWaals radii<br>> ; only used for drawing atoms as balls or for calculating atomic overlap.<br>> ; longest matches are used<br>> ; '???' or '*' matches any residue name<br>
> ; 'AAA' matches any protein residue name<br>> ??? C 0.15<br>> ??? F 0.12<br>> ??? H 0.04<br>> ??? N 0.110<br>> ??? O 0.105<br>> ??? S 0.16<br>><br>> My questions are<br>
> 1. anything wrong of my simulation procedures ?</div>
<div>In theory, not really. What values of potential energy and maximum force did<br>the energy minimization converge to?</div>
<div>> 2. how to find the clashed molecules ?<br>></div>
<div>Read the information printed to the log file (again, I'm assuming you're seeing<br>LINCS warnings, but you haven't told us what "broke" means!) and watch the<br>trajectory to see where things start to fall apart. As I suggested to someone<br>
earlier, if the crash is happening reasonably early, setting "nstxout = 1" is a<br>useful diagnostic to capture all frames prior to the crash.</div>
<div>-Justin</div>
<div>> Thank you<br>> Lin<br>><br>><br>><br>><br>><br>><br>></div>
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