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<P>David:</P>
<P><I> <BR></I>><I> >/ Dear Gmx'ers:<BR></I>><I> />/
<BR></I>><I> />/ As mentioned in the publication about shell water model,
a shell<BR></I>><I> />/ particle is connected to a dummy atom by a
spring-like connection with<BR></I>><I> />/ the following
relationship:<BR></I>><I> />/ <BR></I>><I> />/ 1.
K=sqr(qS)/(4*PHI*Epsilon*alpha),<BR></I>><I> />/ 2.
rsd=(4*PHI*Epsilon*alpha)*E / qS; (rsd is the distance between
<BR></I>><I> shell<BR></I>><I> />/ and dummy particles at any moment,
and E is refered to electrical field</P>
<P></I>><I> />/ strength).<BR></I>><I> />/ <BR></I>><I> />/
Anyone can tell me where is the definition of two equations
above,<BR></I>><I> />/ especially in the case of* "isotropic
polarization",* in GMX source <BR></I>><I> code.<BR></I>><I> />/
Because in my simulation, what I want to polarized is not a water<BR></I>><I>
/>/ molecule. So I need a definite instruction, any
suggestion?<BR></I>><I> /<BR></I>><I>
>gmx/src/gmxlib/bondfree.c<BR></I>><I> <BR></I>><I> In this file,
I can only locate the definition of K, and where is <BR></I>><I> the formula
for calculating rsd? Pls see the following code, it is <BR></I>><I> refered
to the case of isotropic polarization, ok?<BR></I>rsd is the input for the
equation, as it is just the instantaneous <BR>distance between shell and
particle.<BR>><I> <BR></I>><I> <BR></I>><I>
############################################################<BR></I>><I> real
polarize(int nbonds,<BR></I>><I>
t_iatom forceatoms[],t_iparams
forceparams[],<BR></I>><I> rvec
x[],rvec f[],t_forcerec *fr,t_graph
*g,<BR></I>><I> matrix box,real
lambda,real *dvdlambda,<BR></I>><I>
t_mdatoms *md,int ngrp,real egnb[],real
egcoul[],<BR></I>><I> t_fcdata
*fcd)<BR></I>><I> {<BR></I>><I> int
i,m,ki,ai,aj,type;<BR></I>><I> real
dr,dr2,fbond,vbond,fij,vtot,ksh;<BR></I>><I> rvec
dx;<BR></I>><I> ivec dt;<BR></I>><I>
<BR></I>><I> vtot = 0.0;<BR></I>><I> for(i=0;
(i<nbonds); ) {<BR></I>><I> type =
forceatoms[i++];<BR></I>><I> ai =
forceatoms[i++];<BR></I>><I> aj =
forceatoms[i++];<BR></I>><I> ksh =
<BR></I>><I>
sqr(md->chargeT[aj])*ONE_4PI_EPS0/forceparams[type].polarize.alpha;<BR></I>><I>
###############################################################<BR></I>><I>
<BR></I>><I> <BR></I>><I> <BR></I>><I>
<BR></I>><I> <BR></I>><I> <BR></I>><I> >/
<BR></I>><I> />/ Secondly, how can I read the calculated value of spring
constant K by<BR></I>><I> />/ GMX after I defined "alpha" and "qS"? Can
"debug" realize it? If yes,<BR></I>><I> />/ how? Although I have used GMX
for a long time, but that is the first<BR></I>><I> />/ time for me to
encounter such a problem.<BR></I>><I> /<BR></I>><I> >gmxdump -s
topol.tpr | less<BR></I>><I> >search for POL<BR></I>><I> Yes, I
can find the defined value for "polarization: alpha", is it <BR></I>><I>
possible for me to know the calculated value of spring constant K? If
<BR></I>><I> yes, how?<BR></I></P>
<P>> It is not printed anywhere. If you want to see it you have to turn on
<BR>> the debug flag for mdrun.<BR></P>
<P>Very sorry to bother you again, could you point it out much more detailed? I
have never used the "-debug" flag.</P>
<P>For example, in original, I used "mdrun -v -s full -e full -o full -c
after_full -g full" to run my simulation. </P>
<P>Where should "-debug" flag put in? And, where or which file can I find the
calculated value of spring constant K? </P>
<P>Thanks, but I am actually lost to this point.</P>
<P> </P>
<P> </P>
<P>Xie Yinghong</P>
<P>Hong Kong Univ.</P>
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