While minimising ethylene glycol, I have no defines, and constraints are set to none. During equilibration, define is set to -DFLEXIBLE, and constraints are set to all-angles. Which parameters would affect hydrogen bonding?<br>
<br>I have one glycerol molecule in the center of a box of 609 water molecules; what type of thermostat is reasonable for such a system?<br><br><br>Nancy<br><br><br><br><div class="gmail_quote">On Sat, Aug 8, 2009 at 3:49 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 class="im"><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 have successfully minimised and equilibrated ethylene glycol in a water box. I have noticed that there seem to be no hydrogen bonds between the solute and solvent, but there are hydrogen bonds forming and breaking between solvent molecules. Is this a normal behavior during minimsation and equilibration?<br>
<br>
</blockquote>
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That will depend on whether or not you are position-restraining your ethylene glycol, and whether or not your parameters are consistent with the derivation of the force field.<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 converged to machine precision in 7007 steps,<br>
but did not reach the requested Fmax < 10.<br>
Potential Energy = -3.3459230e+04<br>
Maximum force = 4.9560604e+01 on atom 4<br>
Norm of force = 3.4399371e+00<br>
===============================================================<br>
<br>
As I believe these forces to be acceptable, I proceed to equilibration:<br>
<br>
</blockquote>
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These values appear to be reasonable, yes.<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;">
$ grompp -f nvt.mdp -c em.gro -p glycerol.top -o nvt.tpr<br>
<br>
where my "nvt.mdp" file is:<br>
</blockquote>
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</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
rvdw = 1.3<br>
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As I've said before, this value of rvdw is not what is expected when using the G53a6 parameter set. Unless you've got a good reason for altering the original force field specifications, generally this is not a good idea.<div class="im">
<br>
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<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
tcoupl = V-rescale<br>
tc-grps = GOL SOL<br>
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How many glycerol molecules do you have? If it is only a small fraction of the system, this treatment of thermostats is likely not appropriate. See here:<br>
<br>
<a href="http://oldwiki.gromacs.org/index.php/thermostats" target="_blank">http://oldwiki.gromacs.org/index.php/thermostats</a><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;">
===============================================================<br>
Step 0, time 0 (ps) LINCS WARNING<br>
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The procedure for solving a LINCS warning is always the same. Identify where things start to fall apart, then verify that your topology is correct, and your .mdp parameters are reasonable. I've made a few comments on .mdp parameters above. As for the topology, that still remains a mystery. Having never used topolbuild, I don't know how it assigns parameters, so it may work just fine. But in general, this is always part of the diagnosis.<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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