Gromacs

Changing a 3 Point Water Model to a 4 Point Water Model

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    If you have a .gro file that has a 3 point water model and you want to keep the coordinates of the water but change to a 4 point water model, follow the steps below.

     

    1. cat a.gro |awk '{print $0; if($2=="HW2")printf("%8s     MW %4d%8.3f%8.3f%8.3f\n",$1,$3,$4,$5,$6)}' > b.gro
    2. modify the number of atoms in the second line of the file b.gro
    3. editconf -f b.gro -o c.gro
    4. run a short EM on c.gro
    Page last modified 21:13, 8 Jan 2011 by cneale