# [gmx-users] Re: Definition of "polarization"

Yinghong xieyh at hkusua.hku.hk
Thu Dec 15 20:11:32 CET 2005

```David:

> Dear Gmx'ers:
>
> As mentioned in the publication about shell water model, a shell
> particle is connected to a dummy atom by a spring-like connection with
> the following relationship:
>
> 1. K=sqr(qS)/(4*PHI*Epsilon*alpha),
> 2. rsd=(4*PHI*Epsilon*alpha)*E / qS;  (rsd is the distance between shell
> and dummy particles at any moment, and E is refered to electrical field
> strength).
>
> Anyone can tell me where is the definition of two equations above,
> especially in the case of* "isotropic polarization",* in GMX source code.
> Because in my simulation, what I want to polarized is not a water
> molecule. So I need a definite instruction, any suggestion?

>gmx/src/gmxlib/bondfree.c

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?

############################################################
real polarize(int nbonds,
t_iatom forceatoms[],t_iparams forceparams[],
rvec x[],rvec f[],t_forcerec *fr,t_graph *g,
matrix box,real lambda,real *dvdlambda,
t_mdatoms *md,int ngrp,real egnb[],real egcoul[],
t_fcdata *fcd)
{
int  i,m,ki,ai,aj,type;
real dr,dr2,fbond,vbond,fij,vtot,ksh;
rvec dx;
ivec dt;

vtot = 0.0;
for(i=0; (i<nbonds); ) {
type = forceatoms[i++];
ai   = forceatoms[i++];
aj   = forceatoms[i++];
ksh  = sqr(md->chargeT[aj])*ONE_4PI_EPS0/forceparams[type].polarize.alpha;
###############################################################

>
> Secondly, how can I read the calculated value of spring constant K by
> GMX after I defined "alpha" and "qS"? Can "debug" realize it? If yes,
> how? Although I have used GMX for a long time, but that is the first
> time for me to encounter such a problem.

>gmxdump -s topol.tpr | less
>search for POL

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?

Thanks again.

Xie Yinghong
Hong Kong Univ.
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