I tried decreasing emstep, and also tried increasing the number of steps, but I still get the following output from mdrun:<br><br>==================================================<br>Steepest Descents did not converge to Fmax < 1000 in 5001 steps.<br>
Potential Energy = -6.9329155e+03<br>Maximum force = 2.1965221e+04 on atom 39<br>Norm of force = 2.1487129e+03<br>==================================================<br><br>Please advise on how to further decrease the forces.<br>
<br>Thanks,<br><br>Nancy<br><br><br><br><div class="gmail_quote">On Wed, Aug 5, 2009 at 6:08 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="h5"><br>
<br>
Nancy wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
<br>
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:<br>
<br>
==============================<br>
define = -DFLEXIBLE<br>
integrator = steep<br>
emtol = 1000.0<br>
emstep = 0.5<br>
nsteps = 1000<br>
<br>
nstlist = 1<br>
ns_type = grid<br>
rlist = 1.0<br>
coulombtype = PME<br>
rcoulomb = 1.0<br>
rvdw = 1.3<br>
pbc = xyz<br>
<br>
pme_order = 4<br>
constraints = none<br>
==============================<br>
<br>
I process it with grompp, where "ethanediol_solv.gro" is the solvated system, and "ethanediol.top" is the topolgy generated with topolbuild:<br>
<br>
$ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr<br>
<br>
I then run it:<br>
<br>
$ mdrun -v -deffnm em<br>
<br>
mdrun outputs the following information:<br>
<br>
==============================<br>
Steepest Descents did not converge to Fmax < 1000 in 1001 steps.<br>
Potential Energy = -6.7546914e+03<br>
Maximum force = 2.7262363e+04 on atom 34<br>
Norm of force = 2.5032930e+03<br>
==============================<br>
<br>
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.<br>
<br>
</blockquote>
<br></div></div>
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).<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Please advise<br>
<br>
Thanks<br>
<br>
Nancy<br>
<br>
<br>
<br>
<br>
------------------------------------------------------------------------<br>
<br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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