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

Yinghong xieyh at hkusua.hku.hk
Fri Dec 16 01:30:22 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?
rsd is the input for the equation, as it is just the instantaneous
distance between shell and particle.
>
>
> ############################################################
> 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?

> It is not printed anywhere. If you want to see it you have to turn on
> the debug flag for mdrun.

Very sorry to bother you again, could you point it out much more detailed? I have never used the "-debug" flag.
For example, in original, I used "mdrun -v -s full -e full -o full -c after_full -g full" to run my simulation.
Where should "-debug" flag put in? And, where or which file can I find the calculated value of spring constant K?
Thanks, but I am actually lost to this point.

Xie Yinghong
Hong Kong Univ.
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