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<div>Hi </div>
<div>I print out the energy EM-solvated.edr file here.</div>
<div>Since the average is high, is it caused by the molecule clashing?</div>
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<div>I selected potential, kinetic, total energy.</div>
<div>What else energy should I print out to learn the broken simulation system? </div>
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<div>Thank you</div>
<div>Lin</div>
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<div>Select the terms you want from the following list by<br>selecting either the name or the number or a combination.<br>End your selection with an empty line or a zero.<br>---------------------------------------------------------<br>
1 Bond 2 G96Bond 3 Angle 4 G96Angle <br>5 Proper-Dih. 6 Improper-Dih. 7 LJ-14 8 Coulomb-14 <br>9 LJ-(SR) 10 Coulomb-(SR) 11 Potential 12 Kinetic-En. <br>
13 Total-Energy 14 Temperature 15 Pressure-(bar) 16 Vir-XX <br>17 Vir-XY 18 Vir-XZ 19 Vir-YX 20 Vir-YY <br>21 Vir-YZ 22 Vir-ZX 23 Vir-ZY 24 Vir-ZZ <br>
25 Pres-XX-(bar) 26 Pres-XY-(bar) 27 Pres-XZ-(bar) 28 Pres-YX-(bar) <br>29 Pres-YY-(bar) 30 Pres-YZ-(bar) 31 Pres-ZX-(bar) 32 Pres-ZY-(bar) <br>33 Pres-ZZ-(bar) 34 #Surf*SurfTen 35 Mu-X 36 Mu-Y <br>
37 Mu-Z 38 T-rest </div>
<div>11 12 13 0</div>
<div>Back Off! I just backed up 6LYZ-EM-solvated.xvg to ./#6LYZ-EM-solvated.xvg.2#<br>Last frame read 41 time 65.000 </div>
<div>Statistics over 65 steps [ 1.0000 thru 65.0000 ps ], 3 data sets</div>
<div>Energy Average RMSD Fluct. Drift Tot-Drift<br>-------------------------------------------------------------------------------<br>Potential 8.98118e+08 4.53312e+08 0 -3.03617e+07 -1.97304e+09<br>
Kinetic En. 0 0 0 0 0<br>Total Energy 8.98118e+08 4.53312e+08 0 -3.03617e+07 -1.97304e+09</div>
<div>gcq#119: "Bring Out the Gimp" (Pulp Fiction)<br></div>
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<div><br>Chih-Ying Lin wrote:<br>><br>> Hi<br>> The follwing is my .out file.<br>> From it, can I conclude that some molecule clashing with another ?<br>></div>
<div>No, you can conclude that your system is unstable. One possible reason is<br>atomic clashing, but you cannot say for sure. General advice on your problem<br>(which is encountered frequently, and as such, appears thousands of times in the<br>
list archive) can be found on the Gromacs wiki site:</div>
<div><a href="http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings">http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings</a><br><a href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a></div>
<div>If you want further help, take the advice that I gave you before - look at the<br>trajectory, focusing specifically on the problematic atoms (looks like 366 and<br>367 are having problems first, suggesting that either they, or atoms nearby, are<br>
unstable). I also asked about the success of your energy minimization, but you<br>haven't provided that information. From the output, it seems that your<br>simulation is crashing immediately, suggesting that EM did not work properly,<br>
and there *may* be unresolved clashes. You will have to do visual inspection to<br>determine if this is the case.</div>
<div>-Justin</div>
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