On 11/29/12 9:59 AM, juan-manuel.casti...@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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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