[gmx-users] Re: Putting more than one peptide

[alkasrivastava at iitb.ac.in]

Hi

I am doing 5 peptide simulation.

1. First i am defining a box using editconf

editconf -f 1st.gro -o box1.gro -bt cubic -box 6 -d 1.1

then for inserting the next peptide i am using genbox

genbox -cp box1.gro -ci 2nd.gro -nmol 1 -o box2.gro -seed 24 -try 100

and same for the subsequent 3 peptides.

So in this way when i am starting with first peptide i am giving -d option
in editconf for defining the distance between the peptide and the box but
i can not do this when i am inserting 2nd peptide and subsequent 3
peptides.

I am not very sure that if it is correct or not. Also i am not finding any
option in genbox for -d during insertion.

Please suggest what is the best way.