[gmx-users] Energy Minimisation and Equilibration Problems
Justin A. Lemkul
jalemkul at vt.edu
Thu Aug 6 04:34:13 CEST 2009
> I am trying to run equilibration on my solvated ethylene glycol
> (ethanediol) system. I started with an ethanediol mol2 file from which
> topolbuild generated various files. I used editconf to enlarge to box
> of the "ethanediol.gro" file:
> $ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5
> and then I used genbox to solvate it:
> $ genbox -cp ethanediol_box.gro -cs spc216.gro -shell 1 -o
> ethanediol_solv.gro -p ethanediol.top
> I ran energy minimisation on it:
> $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr
> my minim.mdp file is:
> and the energies converge (although I think that the values are still
> too large for this system):
> Steepest Descents converged to Fmax < 1000 in 12 steps
> Potential Energy = -1.1206108e+04
> Maximum force = 9.4016180e+02 on atom 31
> Norm of force = 3.4989252e+02
This all seems reasonable to me.
> nsteps = 5000
> dt = 0.0002
As I said before, 1 ps is too short to be meaningful for just about every system.
> rvdw = 1.3
Also, if using Gromos96, this value of rvdw is not strictly correct for this
> the system "blows up". Addtionally, the structure of the solute is
> incorrect (all atoms are bonded to each other).
Are you still getting LINCS warnings? If so, try "constraints = all-bonds"
instead of "constraints = all-angles." With respect to the "bonds" they are
simply an artefact of whatever visualization software you are using. Bonds are
not formed and broken in classical MD. Again I ask, when looking at the
trajectory, are you compensating for periodic boundary conditions properly using
> Please advise on how to minimise such a system further, and as to why
> the equilibration is so unstable.
> Thank you.
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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