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 ..
Correct.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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