Nancy wrote:
Hello,
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
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 think this is the root of your problem. The maximum force is far too high.
Decrease your value of emstep (the default of 0.01 is generally fine), and try
again. You will not likely see large changes over the course of the trajectory.
EM makes small changes to optimize geometry, hydrogen bonding, etc. There are
no dynamics (remember that EM is essentially conducted at 0 K).
-Justin
Please advise
Thanks
Nancy
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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