Hello everyone, I have a question on LJ and coulomb 1-4 energy terms. These are considered as intramolecular interactions and LJ and coulomb SR as intermolecular. If nrexcl in top file is 3, this means we obtain 1-4 energies, 1-5, 1-6,.... Now what we calculate as intermolecular (SR) contributions includes 1-5, 1-6,.. right? and 1-4 are listed separetely in g energy list.
so to get energies between particles one needs to ecxlude 1-5, 1-6 ...on each molecule? also I would like to know what is specefic with 1-4 interactions, whay are they listed separately. I mean why do we have not 1-5 for instance? Please Let me ask two more simple questions about solvating a molecule. I am using genbox to solvate a solute. I have solute.gro and solvent.gro. What should be the dimension of box in solvent.gro if i want to put -nmol numbers in the solute box. Does it matter what size the box of solvent is (last line in gro)? I have solvated the solute with 50 moleecules of solvent. I have the structure file obtained from genbox. To run em or MD I need to have top file. so I am using pdb2gmx and I get a top file for the solute and 50 solvents but I have one moleculetype (named protein by default). I am confused If I need to have 2 molecuels types for solute and solvent, also if I need to enter the number of solvent molecules at the end of the top file [mols] option, or what I have now is fine and I can proceed to em and md usuing mdp files? :) Thanks for your help.
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