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<DIV>David:</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>><I> > David:<BR></I>><I> > <BR></I>><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
<BR></I>><I> 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
<BR></I>><I> given to<BR></I>><I> > />>/ shell, and doing a
normal dynamcis) in the center of this <BR></I>><I> hexagon,
in<BR></I>><I> > />>/ which shell particle is connected to dummy
through your defined</DIV>
<DIV></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
<BR></I>><I> 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,<BR></I>><I> > What I /<BR></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,</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 <BR></I>><I> 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</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>><I>
> /<BR></I>><I> > > Just realized that I repeated your
calculation and got the same <BR></I>><I> result.<BR></I>><I>
> > How about exclusions? Have you checked the tpr file for
that?<BR></I>><I> > <BR></I>><I> > Firstly, thanks for
your calculating in person. Which result did you<BR></I>><I> > get,
0.1nm or 0.01nm?<BR></I>><I> >See above.<BR></I>><I>
<BR></I>><I> > <BR></I>><I> > In my simulation, I did
not define the exclusions in top file. Instead,<BR></I>><I> > I
defined two energy groups in mdp file: SHELL & Others. Here,
I<BR></I>><I> > wanna check whether the movement of shell particle
is only related to<BR></I>><I> > external field in the absence of
any other non-bonded interations<BR></I>><I> > between shell and
other atoms. So, I defined "energygrp_excl = SHELL <BR></I>><I> >
Others" in mdp files. Is that right?<BR></I>><I> >Maybe, but I'm not
sure.<BR></I>><I> <BR></I>><I> <BR></I>><I> >
<BR></I>><I> > Besides, I checked the tpr file, which seems
ok.<BR></I>><I> >Does this mean that all exclusions were
there?<BR></I>><I> >Is there interaction energy between shell and
others in the output edr <BR></I>><I> file?<BR></I>><I>
<BR></I>><I> Some other information should be useful for your help. Actually,
I have <BR></I>><I> succeeded in defining such a shell model previously. In
those <BR></I>><I> simulations, I set polarizability alpha = 0.05 nm^3,
qS = 0.6e and mSH <BR></I>><I> = 10 a.u., from which the movement of shell
particles are linearly <BR></I>><I> proportional to the external field and
agree with theoretical result. <BR></I>><I> But, When I change the values of
alpha and qS to the current case (alpha <BR></I>><I> = 0.3 nm^3, and qS =
3e), I can not get a satisfied result any more. Do <BR></I>><I> you have any
suggestion to this point?<BR></I></DIV>
<DIV>> no, but try running an energy minimization and check the final
coordinates.</DIV>
<DIV> </DIV>
<DIV>What did you mean about checking the final coordinates?</DIV>
<DIV> </DIV>
<DIV>Yes, you remind me, energy can not converge during EM process. Because, for
some particular reason, during my simulation, I completely fixed the benzene
atoms and make shell particles only move along the direction of electric field.
So, as I think, the reason for no converging of energy is from no changes of
energy during EM. Is it right?</DIV>
<DIV> </DIV>
<DIV>Thanks again for your kind help, but I am actually lost in this point,
which stopped my job from going on.</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>Xie Yinghong<BR></DIV>
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