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<DIV>David:</DIV>
<DIV> </DIV>
<DIV>><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 shell <BR></I>><I> and dummy
particles at any moment, and E is refered to electrical field <BR></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 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></DIV>
<DIV>>gmx/src/gmxlib/bondfree.c</DIV>
<DIV> </DIV>
<DIV>In this file, I can only locate the definition of K, and where is
the formula for calculating rsd? Pls see the following code, it is
refered to the case of isotropic polarization, ok?</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>############################################################</DIV>
<DIV>real polarize(int nbonds,<BR> t_iatom
forceatoms[],t_iparams forceparams[],<BR>
rvec x[],rvec f[],t_forcerec *fr,t_graph
*g,<BR> matrix box,real lambda,real
*dvdlambda,<BR> t_mdatoms *md,int ngrp,real
egnb[],real egcoul[],<BR> t_fcdata
*fcd)<BR>{<BR> int i,m,ki,ai,aj,type;<BR> real
dr,dr2,fbond,vbond,fij,vtot,ksh;<BR> rvec dx;<BR> ivec dt;</DIV>
<DIV> </DIV>
<DIV> vtot = 0.0;<BR> for(i=0; (i<nbonds); )
{<BR> type = forceatoms[i++];<BR>
ai = forceatoms[i++];<BR> aj =
forceatoms[i++];<BR> ksh =
sqr(md->chargeT[aj])*ONE_4PI_EPS0/forceparams[type].polarize.alpha;</DIV>
<DIV>###############################################################</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV><BR> </DIV>
<DIV> </DIV>
<DIV><BR>><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></DIV>
<DIV>>gmxdump -s topol.tpr | less<BR>>search for POL<BR></DIV>
<DIV>Yes, I can find the defined value for "polarization: alpha", is it possible
for me to know the calculated value of spring constant K? If yes, how?</DIV>
<DIV><BR>Thanks again.</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>Xie Yinghong</DIV>
<DIV>Hong Kong Univ.</DIV><I></I></BODY></HTML>