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. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
