[gmx-users] some molecule clashing with another ?

Mark Abraham Mark.Abraham at anu.edu.au
Thu Dec 31 02:32:49 CET 2009


Chih-Ying Lin wrote:
>  
>  
> Hi
> I print out the energy EM-solvated.edr file here.
> Since the average is high, is it caused by the molecule clashing?

It means there's something badly wrong. For the usual sort of 
biomolecular MD simulation, PE should be negative, around 10^-4 to 10^-6 
kJ/mol depending on force field and system size. Thus in your case, at 
least one contribution is probably very large and positive. If you look 
at all the contributions to the energy (easiest in your .log file), you 
will see that the LJ is very large and positive (go check it!) which can 
only happen when atoms are unrealistically close to each other.

> I selected potential, kinetic, total energy.
> What else energy should I print out to learn the broken simulation system? 

Work out what the terms are, and then use your chemical to knowledge to 
see if any of them are meaningful here :-)

Mark

> Thank you
> Lin
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> 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)
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> 
> 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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