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

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 13 19:25:14 CET 2009

Molecular Dynamics wrote:
> Dear All,
> I'm 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 

In general, the topol.top should consist of the #include statements for each 
.itp file, then the [ system ] directive should contain a count of each molecule.

Use editconf to set your box size, and genbox -ci -nmol to insert what you need.

> 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 

If these come from PRODRG, they will probably require manual modification and 
validation of their contents.

> work directories. Then chose one directory ( X ) and do the operations 
> like in ''GROMACS Tutorial for Drug – Enzyme Complex'' Then in this command
> genbox –cp X.pdb –cs Y.pdb –o gmx.pdb –p gmx.top

If you are using X as the solute and Y as the solvent, then yes, this is fine. 
It is just like solvating a protein in water (if X = protein, Y = water).

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



> Could you please help me to learn the true process of using more than 
> one type of molecules in gromacs ?
> Sincerely
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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