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

Justin Lemkul jalemkul at vt.edu
Fri Nov 30 20:29:12 CET 2018

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 A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129


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