GROMACS version: 5.1.4
GROMACS modification: Yes/No
Dear Justin,
I want to simulated three different systems (each system contain a typical solute). How do I solve them in water so that is scientifically correct? Is it true that I use flags “-d 1.0” and “-bt box type” for solving? In this case I will have three systems with different numbers of water molecules. Is it possible to compare the structural and thermodynamic properties of these three different solutes while they solving in different number of water molecules? Should the number of water molecules necessarily be the same in all systems and use “-box x y z” flag in “gmx editconf” and then “-maxsol” flag in “gmx solvate”? These three solutes are nanotube and its derivatives.
Best regrads,
Ganj
Hi Ganj,
No, you don’t need and should not enforce the same number of water molecules in your system.
To be able to compare the simulation setups you want to have the same thermodynamics, i.e. temperature and pressure control, and a distance from the periodic images that ensures that there are no errors in the simulation stemming from self-interaction of a particle with its periodic image.