[gmx-users] Frozen groups lead to a high energy

[Sam David]

Dear Justin,
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.
Any ideas

Best


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
> Dih.
> >      2.07807e+08    2.96662e+05    8.57456e+02    2.50326e+04
> 1.60567e+02
> >            LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb
> (SR)
> >      4.33776e+04   -7.73429e+03    3.05165e+11   -1.07225e+04
>  -1.24055e+07
> >     Coul. recip.      Potential    Kinetic En.   Total Energy
> Temperature
> >      5.93613e+03    3.05360e+11    1.97149e+05    3.05361e+11
> 3.88708e+02
> >   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
> option!
>
> Freezing is an artificial perturbation that, in your case, may be
> preventing an unfavorable clash from being resolved.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
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