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

David van der Spoel spoel at xray.bmc.uu.se
Thu Dec 15 08:42:04 CET 2005

```Yinghong wrote:
> 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.

>
> Thanks again.
>
>
>
> Xie Yinghong
> Hong Kong Univ.
> //
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

```