[gmx-users] generation of guanidium intramolecular force-field

[Mark Abraham]

> Thanks for providing the insight about it. I have tried it.
> I have two query..
> (1) As in the case of simulation with urea as a solute and water as
> solvent the corresponding file urea+h2o.gro file is given there.I have to
> do simulation similar to urea i.e. guanidium ion as a solute in place of
> urea.So in that case how will i be able to create Gdm+h2o.gro file
> analogous to urea+h2o.gro(Gdm=Guanidium ion).

This is what genbox is for.

> (2) If i have to perform simulation with varying concentration of
> system(Guanidium & water), so how will i be able to do it.As i have seen
> in case of urea+h2o.gro concentration of system is fixed and if i have to
> generate a system of different molal(different ratio of urea and water),
> so will be play with concentration.

Do some back-of-the-envelope calculations about how many solvent molecules
you will need for the concentrations you want. It will not be feasible to
have more than a few (tens of) thousands of solvent molecules.

Mark