[gmx-users] energy contributions / question about solvating

jojo J joojoojooon at gmail.com
Thu Jul 8 05:17:22 CEST 2010

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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