[gmx-users] How to define the center of mass for a droplet consisting of different ions and molecules?

[Justin Lemkul]

On 3/3/15 5:59 AM, Kester Wong wrote:
> Dear all,
>
>
> I would like to construct a code to describe the center of mass of a droplet,
> with water and ions.
>
> For the following GROMACS trajectory file (confout.gro), we can have water
> coordinates as:
>
>     57SOL     OW   36289  17.563  14.835   0.520
>
>     57SOL    HW1  36290  17.602  14.916   0.487
>
>     57SOL    HW2  36291  17.571  14.843   0.615
>
>     58SOL     OW   36292  17.588  14.547   0.457
>
>     58SOL    HW1  36293  17.573  14.642   0.458
>
>     58SOL    HW2  36294  17.521  14.512   0.516
>
>     59SOL     OW   36295  11.747  17.611   1.159
>
>     59SOL    HW1  36296  11.714  17.522   1.174
>
>     59SOL    HW2  36297  11.740  17.624   1.064
>
>
> To describe the center of mass of each molecule, we can have the following for-loop:
>
> for i = 1:length(x)/3
>
>     xcm(i) = (x(i*3-2)*massO + x(i*3-1)*massH + x(i*3)*massH)/massWater;
>
>     ycm(i) = (y(i*3-2)*massO + y(i*3-1)*massH + y(i*3)*massH)/massWater;
>
>     zcm(i) = (z(i*3-2)*massO + z(i*3-1)*massH + z(i*3)*massH)/massWater;
>
> end
>
>
> Then, the center of mass of a droplet (100% water) can be defined by:
>
> cmx = sum(xcm)/length(x)*3;
>
> cmy =sum(ycm)/length(y)*3;
>
> cmz = sum(zcm)/length(z)*3;
>
>
> For a droplet consisting of H2O, H3O, and Chloride ions, how does one describe
> the center of mass of each molecule/ion using the for-loop, and then using the
> xcm(i), ycm(i), and zcm(i) to determine the center of the droplet?
>
>

Look at the code for gmx traj.  It does these calculations with gmx traj -ox 
-com.  Save some time and use existing software rather than reinventing the wheel :)

-Justin

>
> Below is an example of the coordinate file:
>
>   2015SOL     OW  42163  17.143  16.975   0.502
>
>   2015SOL    HW1  42164  17.175  17.038   0.567
>
>   2015SOL    HW2  42165  17.222  16.937   0.464
>
>   2016SOL     OW  42166  16.088  17.097   0.778
>
>   2016SOL    HW1  42167  16.094  17.182   0.734
>
>   2016SOL    HW2  42168  16.159  17.098   0.843
>
> .
>
> .
>
> .
>
>   2035H3O     OW  42241  17.895  20.054   0.561
>
>   2035H3O    H31  42242  17.836  20.100   0.492
>
>   2035H3O    H32  42243  17.970  20.114   0.593
>
>   2035H3O    H33  42244  17.930  19.964   0.527
>
>   2036H3O     OW  42245  13.948  17.327   0.503
>
>   2036H3O    H31  42246  13.875  17.348   0.571
>
>   2036H3O    H32  42247  13.978  17.410   0.452
>
>   2036H3O    H33  42248  14.026  17.276   0.544
>
> .
>
> .
>
> .
>
>   2037CLA     CL  42249  13.862  17.882   1.754
>
>   2038CLA     CL  42250  16.686  17.457   0.667
>
>
>
>
> Thanks in advance.
>
> Regards,
> Kester
>
>
>
>
>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================