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<DIV>David:</DIV>
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<DIV>> David:<BR>> <BR>> >/ Yinghong wrote:<BR>>
/>/<BR>> />>/ David:<BR>> />>/<BR>> />>/
>/ Dear Dr. David:<BR>> />>/ />/<BR>> />>/ />/
According to the shell water model, I used this method to another<BR>>
/>>/ kind of molecule, which is composed of 6 atoms (e.g.
benzene).<BR>> />>/ Initially, I put a dummy and shell particle (a
small mass is given to<BR>> />>/ shell, and doing a normal dynamcis) in
the center of this hexagon, in<BR>> />>/ which shell particle is
connected to dummy through your defined<BR>> />>/ isotropic
polarization method.<BR>> />>/ />/<BR>> />>/ />/
Theoretically, polarization can be looked as a spring-like<BR>> />>/
connection with constant Kr = sqr(qS)/4*PHI*Epsilon*Alpha, and the<BR>>
/>>/ distance between dummy and shell particle can be decided by rsd
=<BR>> />>/ 4*PHI*Epsilon*Alpha * E0 / qS. Is it right?<BR>>
/>>/ />/<BR>> />>/ />/ Now, in my simulation, I applied an
external electric field along<BR>> />>/ Z direction, and the
interactions (vdws + coulomb) between shell<BR>> />>/ particle and all
the other atoms are exclued. (Of course, here, <BR>> What I /<BR>>
>>/ did is only to make a test instead of a real case). Obviously,
for<BR>> />>/ dummy and shell particles, E0 is currently only referred
to the<BR>> />>/ external field, because local field is
excluded.<BR>> />>/ />/<BR>> />>/ />/
Quantitively, I set alpha = 0.3 nm^3, qS = 3.0e and E0 = 1.5<BR>>
/>>/ V/nm, through "mdrun -debug", alpha and qS can be correctly
output,<BR>> />>/ and the calculated value for Kr = 4168 KJ/mol/nm^2 is
also in the<BR>> />>/ right way. After simulation, I used "g_dist" to
check the distance<BR>> />>/ between dummy and shell particle (rsd)
under such electric field. But<BR>> />>/ the calculted value for rsd is
only 10 percent of the theoretical<BR>> />>/ value although I have
tried for many times.<BR>> />>/ />/<BR>> />>/ />/ So,
Could you tell me some possible errors in my defined model,<BR>> />>/
and why rsd can not approach to the theoretical value? What is the<BR>>
/>>/ principle for GMX to calculate this rsd?<BR>> />>/
/>/<BR>> />>/ /<BR>> />>/ > Isn't the problem nm
vs. Ångström?<BR>> />>/ I am very sure it is not that problem. Upon the
parameters mentioned<BR>> />>/ above, rsd should be ~0.1nm
theoretically, but my calculation gave a<BR>> />>/ value of only
0.01nm. So, any other suggestion?<BR>> />>/ <BR>> />>/
<BR>> />/<BR>> />/<BR>> />/ We have<BR>> />/<BR>>
/>/ F = q E = k r or<BR>> />/ r = q E / k<BR>> />/ r = 0.00108
(eV/kj/mol) nm<BR>> />/ = 0.1 nm<BR>> /<BR>> >
Just realized that I repeated your calculation and got the same
result.<BR>> > How about exclusions? Have you checked the tpr file
for that?<BR>> <BR>> Firstly, thanks for your calculating in person.
Which result did you <BR>> get, 0.1nm or 0.01nm?<BR>>See above.</DIV>
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<DIV>> <BR>> In my simulation, I did not define the exclusions in
top file. Instead, <BR>> I defined two energy groups in mdp file: SHELL &
Others. Here, I <BR>> wanna check whether the movement of shell particle is
only related to <BR>> external field in the absence of any other non-bonded
interations <BR>> between shell and other atoms. So, I defined
"energygrp_excl = SHELL <BR>> Others" in mdp files. Is that
right?<BR>>Maybe, but I'm not sure.</DIV>
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<DIV><BR>> <BR>> Besides, I checked the tpr file, which seems
ok.<BR>>Does this mean that all exclusions were there?<BR>>Is there
interaction energy between shell and others in the output edr file?</DIV>
<DIV> </DIV>
<DIV>Some other information should be useful for your help. Actually, I have
succeeded in defining such a shell model previously. In those simulations, I set
polarizability alpha = 0.05 nm^3, qS = 0.6e and mSH = 10 a.u., from
which the movement of shell particles are linearly proportional to the
external field and agree with theoretical result. But, When I change the values
of alpha and qS to the current case (alpha = 0.3 nm^3, and qS = 3e), I can not
get a satisfied result any more. Do you have any suggestion to this point?</DIV>
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<DIV>Thanks again.</DIV>
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<DIV>Xie Yinghong <BR></DIV></BODY></HTML>