Simulate, Analyse, Plot ...

Molecular dynamics parameters file For energy minimization: em.mdp For NVT simulations: nvt.mdp For NPT simulations: npt.mdp

BINARY MIXTURE Let say someone is interested to study some protein molecules in Water-Ethanol binary mixture. Now the question is how to create binary solvent like this? In Gromacs genbox is very powerful in this context. If ratio does not matter, then one can use the following command genbox_d -cp ethanol.gro -cs spc216.gro -p topol.top -o water_ethanol.gro -box a b c The above commands will fill the simulation box with ethanol and water molecules with random numbers of water molecules and number of ethanol molecules presents in the ethanol.gro file. However, if one is intend to create some exact number percentage of ethanol-water mixture, the following method will be very useful Water-Ethanol binary mixture of defined % Create a .pdb file of single ethanol molecule. (It is very easy, just google it out or create .pdb from software like pymol, prodrg etc., if .gro file is there, no need to create the .pdb file). Convert that .pdb file to .gro file by executing any one of the fol...

Few basic commands: After successful installation you are ready to go with GROMACS. A basic tutorial for simulating Lysozyme in water can be found here . Here, I will compile few necessary commands in one page. Execute .pdb file to generate initial .gro file pdb2gmx -f initial.pdb -o processed.gro If you do not have topology file of your molecule, you can generate one by using g_x2top -f file.gro -o topol.top -ff select -name ABC -noparam -pbc   In the above command line 'ABC ' is your molecule NAME, e.g. if you are simulating carbon nanotube and you are calling carbon nanotube as CNT, then ABC = CNT Define your simulation box using editconf: editconf -f processed.gro -o newbox.gro -c -d 1.0 -bt cubic Solvation of defined box genbox -cp newbox.gro -cs spc216.gro -o newbox_solv.gro -p topol.top Include ions if necessary: grompp -f ions.mdp -c newbox_solv.gro -p topol.top -o ions.tpr genion -s ions.tpr -o newbox_solv_ions.gro -p topol.top -pname NA -...