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<div>HI </div>
<div>I confined one molecule in the center of box and issue the g_dipole command.</div>
<div>The average dipole moment is still around 32. </div>
<div>It is the molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment around 32 too high?<br></div>
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<div>How can I test next and know that the dipole moment around 32 is acceptable?</div>
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<div>Thank you</div>
<div>Lin</div>
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<div>On 2010-10-16 21.36, Chih-Ying Lin wrote:<br>><br>> Hi<br>> I issue the g_dipole command on Gromacs => And, the following<br>> information is shown.<br>> There are 10 molecules in the selection,<br>
> Does the Average =32.1611 refer to the average for a single over the<br>> simulation time?<br>> Or, the Average = 32.1611 summing for all the 10 molecules over the<br>> simulation time?<br>> If the average = 32.1611 for a single molecule with 33 atoms / united<br>
> atoms of most carbon groups, isn't the dipole moment too high?<br>I think this is the average per molecule. You may need to run trjconv<br>-pbc whole, because mdrun may break molecules in two parts, meaning that<br>
the molecule becomes as big as the box.</div>
<div><br>><br>><br>><br>><br>> What does "will subtract their charge at their center of mass" this mean?<br>> Why "will subtract their charge at their center of mass" ?<br>><br>
><br>><br>><br>> ==================================================================<br>> There are 10 molecules in the selection<br>> There are 10 charged molecules in the selection,<br>> will subtract their charge at their center of mass<br>
> Using Volume from topology: 220.317 nm^3<br>><br>> Back Off! I just backed up epsilon.xvg to ./#epsilon.xvg.1#<br>><br>> Back Off! I just backed up aver.xvg to ./#aver.xvg.1#<br>> Last frame 10000 time 20000.000<br>
> Average volume over run is 221.043<br>><br>> Dipole moment (Debye)<br>> ---------------------<br>> Average = 32.1161 Std. Dev. = 2.9926 Error = 0.0095<br>></div>
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