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

[David van der Spoel]

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.
> 
> 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?
mdrun -debug (other options)
you will get a file mdrun.log contaning lots of debug information, 
search for ksh.
> 
> Thanks, but I am actually lost to this point.
> 
>  
> 
>  
> 
> Xie Yinghong
> 
> Hong Kong Univ.
> 
>  
> 
> 
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> 
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-- 
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
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