[gmx-users] about periodicity removal

rama david ramadavidgroup at gmail.com
Sat Feb 25 15:24:03 CET 2012

Hi GROMACS friends,
                         I am trying to put to peptide close to each other..
with the help of -editconf  -ci and  -nmol option ,the peptide can be put
randomly at different location, but they are far apart.
     To solve problem I proceed as  follow...
1. I make gro file , with the -editconf I make box and put molecule in
    I get the box vectors and center co-ordinates.
2. then again with the help of editconf I make a another box of same vectors
   but slightly different center co-ordinates.(Distance is as per my
3 Now have two gro files of box molecule ,having same box vectors and
4 I converted both  gro files to pdb files ,and catenate them to make
single pdb file.
5  Now I get the two molecule close enough to form hydrogen bond..
           but the problem is to convert it again into gro file and
generate topology
file , should I removed periodicity of molecule (As it showing the periodic
box in pymol)???
    If it is , how to remove periodicity???
 Thank you for help....
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