Bruce D. Ray wrote:
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
These last three are not relevant for energy minimization. There are no
velocities, so they can't be generated, and thus there's no temperature
or pressure. nstcomm is probably moot or ignored.
Mark
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.
------------------------------------------------------------------------
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