Nancy wrote:
I tried decreasing emstep, and also tried increasing the number of
steps, but I still get the following output from mdrun:
==================================================
Steepest Descents did not converge to Fmax < 1000 in 5001 steps.
Potential Energy = -6.9329155e+03
Maximum force = 2.1965221e+04 on atom 39
Norm of force = 2.1487129e+03
==================================================
Please advise on how to further decrease the forces.
Figure out what's pushing on atom 39 to generate such a huge force. How to
resolve the problem depends on what's happening. If it's just a poorly-placed
water molecule, you can try deleting that water molecule and trying again.
Beyond that, it will depend on what you find.
-Justin
Thanks,
Nancy
On Wed, Aug 5, 2009 at 6:08 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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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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