I have tried 15,000 steps; I noticed that Fmax starts out at ~3.0e+03 and increases to ~1.2e+06 before coming down very slowly to ~5.0e+04. Additionally, letting the minimisation run for a long time gives me a "converged to machine precision, but not to Fmax < 10" message.<br>
<br>I am wondering why the Lysozyme tutorial at:<br><br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html</a><br>
<br>does not have the same problems?<br><br>Is there a way to stop minimisation and continue later from that same point?<br><br>Thanks,<br><br>Nancy<br><br><div class="gmail_quote">On Thu, Aug 6, 2009 at 6:45 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;"><br>
<br>
Nancy wrote:<br>
<br>
<snip><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Note: the ethanediol.log file contains a section that has several lines with asterisks:<br>
<br>
============================<br>
Angles Force Field Results<br>
Angle Atoms force angle method measured<br>
1 H12- C1- H11 ****** ****** ****** 109.403<br>
</blockquote>
<br></div>
Probably because these angles don't exist in a UA force field, as they involve non-polar hydrogens.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
$ editconf -f ethanediol.gro -o ethanediol_box.gro -c -d 1.0 -bt cubic<br>
<br>
$ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_solv.gro -p ethanediol.top<br>
<br>
$ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr<br>
<br>
the "minim.mdp" file is:<br>
<br>
============================<br>
define = -DFLEXIBLE<br>
integrator = steep<br>
emtol = 10.0<br>
emstep = 0.01<br>
nsteps = 2000<br>
<br>
</blockquote>
<br></div>
Increase the value of nsteps dramatically. If you are aiming for Fmax < 10, 2000 steps likely is not sufficient. Use a ridiculously high value, and if mdrun completes all those steps without converging, keep increasing the value. I typically set nsteps = 500000 to make sure the EM doesn't stop before reaching emtol. If it does, then something may be wrong.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
nstlist = 1<br>
ns_type = grid<br>
rlist = 1.0<br>
coulombtype = PME<br>
rcoulomb_switch = 1.0<br>
</blockquote>
<br></div>
With PME, rcoulomb_switch is meaningless.<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
rvdw_switch = 1.3<br>
</blockquote>
<br>
With the default vdwtype (cutoff), rvdw_switch is also meaningless.<br>
<br>
<snip><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Steepest Descents did not converge to Fmax < 10 in 2001 steps.<br>
Potential Energy = -3.3810168e+04<br>
Maximum force = 5.4957539e+04 on atom 559<br>
Norm of force = 2.7119446e+03<br>
============================<br>
<br>
I have already tried increasing the number of steps, but I found no way <br>
</blockquote>
<br></div>
How many steps did you try?<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
of lowering the forces. I have found that by limiting the number of solvent molecules to ~5, I can manage to acheive lower energies, however, the amount of time it takes for a larger number of water molecules increases exponentially.<br>
<br>
So, I am trying to proceed to equilibration:<br>
<br>
</blockquote>
<br></div>
Stop right here. It is a waste of time. If you EM does not converge, you *cannot* force the system to run. It will explode, sooner or later. Depending on how soon it does will determine how much time you waste.<br>
<br>
At this point, you are really getting the same advice over and over, because the question is always the same, but the values of Fmax are different. Can you post the topology you're using for this system, in particular, the parameters for ethanediol?<br>
<br>
-Justin<br>
<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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