How to grep rows that have certain value in a specific column?

You don't use grep. Use awk.

"your data" | awk '$1 ~ /\.[05]00/'

awk '$1 ~ /\.[50]00/ { print $0 }' myFile.txt

The first column $1 will be matched against /\.500|\.000/ the dots are escaped to be literal dots not regex any character the ~ is partial match, and print the whole line $0

I would like to grep only the rows that have in the first column the decimal .000 and .500

My first thought

grep '^ *[0-9][0-9][0-9]\.[50]00' filename

Quick test using WSL

$ head testdata
              200.000    1.353    0.086
              200.250    1.417    0.000
              200.500    1.359    0.091
              200.750    1.423    0.000
              201.000    1.365    0.093
              201.250    1.427    0.000
              201.500    1.373    0.093
              201.750    1.432    0.000
              202.000    1.383    0.091
              202.250    1.435    0.000
$ grep '^ *[0-9][0-9][0-9]\.[50]00' testdata
              200.000    1.353    0.086
              200.500    1.359    0.091
              201.000    1.365    0.093
              201.500    1.373    0.093
              202.000    1.383    0.091
              202.500    1.392    0.087
              203.000    1.402    0.081
              203.500    1.412    0.073
              204.000    1.423    0.065
              204.500    1.432    0.055
              205.000    1.441    0.045

There are more concise ways to express this.

$ grep -E '^ *[0-9]{3}\.[50]00' testdata
              200.000    1.353    0.086
              200.500    1.359    0.091
              201.000    1.365    0.093
              201.500    1.373    0.093
              202.000    1.383    0.091
              202.500    1.392    0.087
              203.000    1.402    0.081
              203.500    1.412    0.073
              204.000    1.423    0.065
              204.500    1.432    0.055
              205.000    1.441    0.045

If the first column may have other than a 3-digit integer part

grep -E '^ *[0-9]+\.[05]00' testdata

Under some circumstances you might need to use [:digit:] in place of [0-9].

And so on.

man grep is your friend.