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

Justin Lemkul jalemkul at vt.edu
Thu Nov 29 16:11:51 CET 2012

On 11/29/12 9:59 AM, juan-manuel.castillo at mv.uni-kl.de wrote:
> 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:
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
> 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
>      1.66069e+10
> 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?

Can you post a complete .mdp file?  In theory, if one evaluates the same 
configuration under the same parameters (i.e. in a single-point energy 
evaluation), yes, the energies reported should be the same.  But doing EM and 
doing MD are not the same, especially if you are introducing constraints or 
other parameters.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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