[gmx-users] Potential energy from a previous configuration mismatch

juan-manuel.castillo at mv.uni-kl.de juan-manuel.castillo at mv.uni-kl.de
Thu Nov 29 15:59:01 CET 2012

Dear Gromacs friends,

I am running some simulations of a hexane/ethanol mixture 
in a box, using a United-Atom OPLS model. My Gromacs 
version is the 4.5.5.

I fill the simulation box with genbox (I have also used an 
equilibrated pdb file generated by other simulation code), 
and I run a energy minimization simulation, wich gives the 
following energies for the final configuration:

    Energies (kJ/mol)
           Angle   Fourier Dih.          LJ-14 
    Coulomb-14        LJ (SR)
     6.62915e+00    5.17493e+02   -2.61388e+01 
   0.00000e+00   -4.01422e+03
   Disper. corr.   Coulomb (SR)       RF excl. 
     Potential Pres. DC (bar)
    -9.65799e+01    0.00000e+00    0.00000e+00 
  -3.61282e+03    0.00000e+00

Potential Energy  = -3.6128213e+03
Maximum force     =  2.7169607e+01 on atom 541
Norm of force     =  3.9986315e+00

I take the final configuration, and using exactly the same 
force field definition and simulation parameters (cutoff 
radious, electrostatic method, etc), I start a molecular 
dynamics simulation in the NVE ensemble. No matter what I 
do, I always have a blow-up problem. I have checked all 
the points that could be giving the problem, in particular 
the ones given here:


and I have also tried to modify one by one different 
parameters, but I never succeed to obtain a running 
simulation. I have seen that I always have a much larger 
energy at the beginning of the simulation than the energy 
at the end of the minimization:

    Energies (kJ/mol)
           Angle   Fourier Dih.          LJ-14 
    Coulomb-14        LJ (SR)
     5.43743e+04    2.06120e+03    6.02532e+01 
   0.00000e+00    1.62817e+07
   Disper. corr.   Coulomb (SR)       RF excl. 
     Potential    Kinetic En.
    -9.65799e+01    0.00000e+00    0.00000e+00 
   1.63381e+07    1.65906e+10
    Total Energy    Temperature Pres. DC (bar) Pressure 
(bar)   Constr. rmsd

but the potential energy should be exactly the same in 
both cases, as it only depends on the atomic positions. 
Anybody can tell me what I am doing wrong?


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