[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 ?
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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