[gmx-users] using more than one type of molecules

Molecular Dynamics amberquestion at yahoo.com
Fri Mar 13 19:14:20 CET 2009



new to Gromacs and have some questions to learn the answers. I study
on one type molecule.  If I want to add lets say 240 molecules, which
is the best way to use editconf or genbox ? And I learned the
procedure of using more than one type of molecules in gromacs. But
I'm not sure, so I'm waiting for your contributions. Assume that I
have two small organic molecules like hydrocarbons X and Y. I think
First I will have to  get seperately DRGGMX.ITP and DRGPOH.PDB for
the each molecules in different work directories. Then chose one
directory ( X ) and do the operations like in ''GROMACS Tutorial for
Drug – Enzyme Complex'' Then in this command 

–cp X.pdb –cs Y.pdb –o gmx.pdb –p gmx.top 

I get gmx.pdb gmx.top  files I will add #include “Y.itp” and
editing the number of Y molecule and go on ..

you please help me to learn the true process of  using more than one
type of molecules in gromacs ? 


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