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On 04/10/2012 12:00 PM, <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> wrote:
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cite="mid:20120410100006.4105F25C80@struktbio205.bmc.uu.se"
type="cite">
<pre wrap="">On 2012-04-10 11:16, Tom Kirchner wrote:
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<pre wrap=""><span class="moz-txt-citetags">> </span>On 04/10/2012 11:10 AM, <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> wrote:
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<pre wrap=""><span class="moz-txt-citetags">>> </span>On 2012-04-10 09:57, David van der Spoel wrote:
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<pre wrap=""><span class="moz-txt-citetags">>>> > </span> On 2012-04-10 09:43, Tom Kirchner wrote:
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<pre wrap=""><span class="moz-txt-citetags">>>>> >> </span> Hi all,
<span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >> </span> I want to test the g_dipoles tool and made a 20 ns simulation with SPC/E
<span class="moz-txt-citetags">>>>> >> </span> water. Sadly the result for the dielectric constant (e_sim=109.713)
<span class="moz-txt-citetags">>>>> >> </span> looks very different from experimental (e_exp=78) and reported values
<span class="moz-txt-citetags">>>>> >> </span> for SPCE (e_paper=70). I put the command line and the output below.
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<pre wrap=""><span class="moz-txt-citetags">>>> ></span>
<span class="moz-txt-citetags">>>> > </span> Did you run the simulation with PME or at the very least RF?
<span class="moz-txt-citetags">>>> ></span>
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<pre wrap=""><span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >> </span> Gromacs 4.5.3, SPC/E water, 20ns, NPT, 300K, 1bar
<span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >> </span> g_dipoles -corr total -c dipoles -f md_20ns.xtc -s md_20ns.tpr -b 0 -e
<span class="moz-txt-citetags">>>>> >> </span> 20000
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<pre wrap=""><span class="moz-txt-citetags">>>> > </span> You don't need the corr flag for computing the dielectric constant.
<span class="moz-txt-citetags">>>> ></span>
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<pre wrap=""><span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >> </span> #==========================================
<span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >> </span> Using 5 as mu_max and -1 as the dipole moment.
<span class="moz-txt-citetags">>>>> >> </span> WARNING: EpsilonRF = 0.0, this really means EpsilonRF = infinity
<span class="moz-txt-citetags">>>>> >> </span> Selected 0: 'System'
<span class="moz-txt-citetags">>>>> >> </span> There are 1024 molecules in the selection
<span class="moz-txt-citetags">>>>> >> </span> Using Volume from topology: 30.2049 nm3
<span class="moz-txt-citetags">>>>> >> </span> Average volume over run is 30.2103
<span class="moz-txt-citetags">>>>> >> </span> t0 0, t 20000, teller 10001
<span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >> </span> Dipole moment (Debye)
<span class="moz-txt-citetags">>>>> >> </span> ---------------------
<span class="moz-txt-citetags">>>>> >> </span> Average = 2.4883 Std. Dev. = 0.1342 Error = 0.0000
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<pre wrap=""><span class="moz-txt-citetags">>> </span>Another point: the literature value of the dielectric constant for SPC/E
<span class="moz-txt-citetags">>> </span>is for the rigid model. Looks like your using a flexible model here.
<span class="moz-txt-citetags">>></span>
<span class="moz-txt-citetags">>></span>
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<pre wrap=""><span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >> </span> The following averages for the complete trajectory have been calculated:
<span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >> </span> Total< M_x> = 1.45986 Debye
<span class="moz-txt-citetags">>>>> >> </span> Total< M_y> = 5.71202 Debye
<span class="moz-txt-citetags">>>>> >> </span> Total< M_z> = 3.39196 Debye
<span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >> </span> Total< M_x2> = 10964.8 Debye2
<span class="moz-txt-citetags">>>>> >> </span> Total< M_y2> = 10794.4 Debye2
<span class="moz-txt-citetags">>>>> >> </span> Total< M_z2> = 10762.4 Debye2
<span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >> </span> Total< <code class="moz-txt-verticalline"><span class="moz-txt-tag">|</span>M<span class="moz-txt-tag">|</span></code>^2> = 32521.6 Debye2
<span class="moz-txt-citetags">>>>> >> </span> Total |< M>|^2 = 46.2638 Debye2
<span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >> </span> < <code class="moz-txt-verticalline"><span class="moz-txt-tag">|</span>M<span class="moz-txt-tag">|</span></code>^2> - |< M>|^2 = 32475.4 Debye2
<span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >> </span> Finite system Kirkwood g factor G_k = 5.12208
<span class="moz-txt-citetags">>>>> >> </span> Infinite system Kirkwood g factor g_k = 3.43028
<span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >> </span> Epsilon = 109.713
<span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >> </span> #==========================================
<span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >> </span> I would be really grateful if anybody could point me to my error. I
<span class="moz-txt-citetags">>>>> >> </span> attached my .mdp file in case the error lies there.
<span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >> </span> Best regards
<span class="moz-txt-citetags">>>>> >> </span> Tom
<span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >></span>
<span class="moz-txt-citetags">>>>> >></span>
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<pre wrap=""><span class="moz-txt-citetags">>>> ></span>
<span class="moz-txt-citetags">>>> ></span>
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<pre wrap=""><span class="moz-txt-citetags">>> </span>-- David van der Spoel, Ph.D., Professor of Biology
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<pre wrap=""><span class="moz-txt-citetags">> </span>Thank you for your reply,
<span class="moz-txt-citetags">></span>
<span class="moz-txt-citetags">> </span>I used the rigid model. I also used PME, I think this is the error, for
<span class="moz-txt-citetags">> </span>g_dipoles seems to be constructed for reaction field. Is this correct?
<span class="moz-txt-citetags">> </span>I'll redo the simulation with reaction field now.
<span class="moz-txt-citetags">></span>
<span class="moz-txt-citetags">> </span>Best
<span class="moz-txt-citetags">> </span>Tom Kirchner
<span class="moz-txt-citetags">></span>
<span class="moz-txt-citetags">></span>
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<pre wrap="">No! g_dipoles does not care. You may have a remnant command in your mdp
file (-DFLEXIBLE), please remove it. For rigid model there should not
be any fluctations in the dipole.
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Many Many thanks for your help, there was an error in the topology
file. <br>
<br>
I am wondering, why the flexibility of SPC/E water has such a big
effect on the dielectric constant. Also, which formula or method
does g_dipoles use to calculate the dielectric constant. In the
mailing list you refer to a JCP paper of 1998 by you, but there only
a formula for reaction field is given.<br>
<br>
Best<br>
Tom<br>
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