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