[gmx-users] Frozen groups lead to a high energy
samdav800 at gmail.com
Fri Nov 30 21:47:52 CET 2018
Thank you for your answer.
I will try position restraints which could be better for my case but I'm
not sure how to get force constants.
On Fri, Nov 30, 2018 at 1:29 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> On 11/29/18 6:23 PM, Sam David wrote:
> > Dear gromacs users
> > I'm simulation a hydrocarbon and water mixture placed on a slab of metal.
> > The metal surface is frozen in the z-direction. Energy minimization works
> > with no errors but I see the potential energy is too high as below.
> > Steepest Descents converged to machine precision in 1754 steps,
> > but did not reach the requested Fmax < 1.
> > Potential Energy = 1.9604517e+08
> > Maximum force = 3.1745122e+03 on atom 23433
> > Norm of force = 3.8078518e+01
> > After energy minimization, I did short nvt followed by short npt then npt
> > production. I tried several times and different parameters to reduce the
> > energy of the system but still very high as below:
> > Energies (kJ/mol)
> > Bond Angle Proper Dih. Ryckaert-Bell. Improper
> > 2.07807e+08 2.96662e+05 8.57456e+02 2.50326e+04
> > LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb
> > 4.33776e+04 -7.73429e+03 3.05165e+11 -1.07225e+04
> > Coul. recip. Potential Kinetic En. Total Energy
> > 5.93613e+03 3.05360e+11 1.97149e+05 3.05361e+11
> > Pres. DC (bar) Pressure (bar) Constr. rmsd
> > -2.71515e+02 3.08812e+10 4.72857e-06
> > However, when I remove frozen groups, potential energy becomes negative
> > Any ideas on how to reduce system energy while using freeze groups
> Freezing is an artificial perturbation that, in your case, may be
> preventing an unfavorable clash from being resolved.
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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