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