[gmx-users] Frozen groups lead to a high energy
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.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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