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