On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy <[email protected]> wrote:
> 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:
>
> ==========================
> define = -DFLEXIBLE
> integrator = steep
>
emtol = 1000.0
> emstep = 0.01
> nsteps = 5000
>
> nstlist = 1
> ns_type = grid
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> rvdw = 1.3
> pbc = xyz
>
> pme_order = 4
> constraints = none
>
> nstxout = 1
> nstvout = 1
> nstenergy = 1
> nstlog = 1
> ==========================
>
> $ mdrun -v -deffnm em
>
> 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
> ==========================
{remainder snipped}
The energies do seem large. What happens if you do energy minimization
with emtol = 10.0 ?
--
Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
>
>From: Nancy <[email protected]>
>To: Discussion list for GROMACS users <[email protected]>
>Sent: Wednesday, August 5, 2009 10:28:47 PM
>Subject: [gmx-users] Energy Minimisation and Equilibration Problems
>
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