[gmx-users] problem regarding editconf

[Mark Abraham]

> hi all,
> i have one problem regarding 'editconf' for using add simulation box, my
> protein contain 59 residues + crystal water -103 molecules
> In one tutorial they have used following command for add simualation box
> 1.editconf  ­bt cubic –f fws.pdb –o fws.pdb –d 0.9    - in this 0.9 is nm

Please be accurate. The above command line was not what the tutorial will
have had - rather "editconf -bt cubic" etc.

>  i have reffered in gmxusers(archives) they have used following command
> for
> adding simulation box and water
>  1. editconf -f popc128a.pdb -o po_box.pdb -box 6.1065 6.1059 9.0000 -c
>  2. genbox  -cp  po_box.pdb  -cs  -o  po_sol.pdb  -p  lip.top
>
> based on above things i have used following commands for adding simulation
> box and water
>
> 1.editconf  ­bt cubic –f fws.pdb –o fws.pdb –d 0.4    - in this 0.4 is nm

Using the same file name for input and output is asking for trouble.

> 2. genbox  -cp  po_box.pdb  -cs  -o  po_sol.pdb  -p  prot.top
> program was finished without error and it added 4884 water molecules
> around
> my protein
> is it right, what i have done  or any  chages i have to  do?

That depends what you want the simulation to do. 0.4nm margins are so
small that your periodic copies will be interacting with each other. This
is unrealistic. Check out some textbook material here.

Mark