On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy <nancy5vi...@gmail.com> wrote:
> I was trying to run equilibration on my solvated ethylene glycol
system. However, the
> system seems to be "exploding". I believe this
is due to inadequate energy minimisation,
> however, I am unable to
minimise my system any further. I am using the following .mdp
> file
"minim.mdp" for minimsation:
>
> ==============================
> define = -DFLEXIBLE
> integrator = steep
> emtol = 1000.0
> emstep = 0.5
> nsteps = 1000
I use more steps than 1000 (may want 10000) with:
emstep = 0.01
nstcomm = 1
Tcoupl = no
Pcoupl = no
gen_vel = no
>
> nstlist = 1
> ns_type = grid
> rlist = 1.0
>
coulombtype = PME
> rcoulomb = 1.0
> rvdw = 1.3
> pbc = xyz
>
> pme_order = 4
> constraints = none
> ==============================
>
> I
process it with grompp, where "ethanediol_solv.gro" is the solvated
system,
> and "ethanediol.top" is the topolgy generated with topolbuild:
>
> $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr
>
> I then run it:
>
> $ mdrun -v -deffnm em
>
> mdrun outputs the following information:
>
> ==============================
> Steepest Descents did not converge to Fmax < 1000 in 1001 steps.
>
Potential Energy = -6.7546914e+03
> Maximum force = 2.7262363e+04 on atom 34
> Norm of force = 2.5032930e+03
> ==============================
>
> I
have viewed the output trajectory of the minimisation and I can see
that the
> waters do not move much. I am wondering if there is a way to
let solvent water
> molecules move about during minimsation, and/or how
to remove some of them.
> I am also unsure what value of emtol is
reasonable for this type of small system.
I use the same value of emtol, but that's just based on examples I've seen where
others have used that value.
--
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 <nancy5vi...@gmail.com>
>To: Discussion list for GROMACS users <gmx-users@gromacs.org>
>Sent: Wednesday, August 5, 2009 6:03:51 PM
>Subject: [gmx-users] Energy Minimisation Values
>
>
>
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