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On 04/10/2012 11:10 AM, <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> wrote:
<blockquote
cite="mid:20120410091042.20BB625C83@struktbio205.bmc.uu.se"
type="cite">
<pre wrap=""><div class="moz-txt-sig">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>
</pre>
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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
</pre>
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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="">Another point: the literature value of the dielectric constant for SPC/E
is for the rigid model. Looks like your using a flexible model here.
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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="">
<div class="moz-txt-sig">--
David van der Spoel, Ph.D., Professor of Biology
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Thank you for your reply,<br>
<br>
I used the rigid model. I also used PME, I think this is the error,
for g_dipoles seems to be constructed for reaction field. Is this
correct?<br>
I'll redo the simulation with reaction field now.<br>
<br>
Best<br>
Tom Kirchner<br>
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