[gmx-users] some molecule clashing with another ?

Chih-Ying Lin chihying2008 at gmail.com
Thu Dec 31 02:23:14 CET 2009

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

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
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
Potential                8.98118e+08 4.53312e+08          0 -3.03617e+07
Kinetic En.                       0          0          0
0          0
Total Energy             8.98118e+08 4.53312e+08          0 -3.03617e+07
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
(which is encountered frequently, and as such, appears thousands of times in
list archive) can be found on the Gromacs wiki site:
If you want further help, take the advice that I gave you before - look at
trajectory, focusing specifically on the problematic atoms (looks like 366
367 are having problems first, suggesting that either they, or atoms nearby,
unstable).  I also asked about the success of your energy minimization, but
haven't provided that information.  From the output, it seems that your
simulation is crashing immediately, suggesting that EM did not work
and there *may* be unresolved clashes.  You will have to do visual
inspection to
determine if this is the case.
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