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?
Thanks
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