[gmx-users] X.gro file for different solvent system

[kinshuk at chem.iitb.ac.in]

Hi all,
  I have a query regarding making .gro file for different solvent system.
In SPC216.gro & MeOH.gro there is 216 water/MeOH molecules are there.In
dmso.gro 208 molecules are there.In urea+h2o.gro 36 urea & 357 water
molecules are there with particular box size.I couldn't understand what is
the basic logic behind that?
  I have to make the solvent system of guanidium ion + thiocynate ion +
Water molecule.I have to use different box size & different
concentration (6molal,7 molal).So how will i judge how many ions & water
molecule in the X.gro file like urea+h2o.gro.Is it a particular ratio
between urea & water molecules for particular concentration ? If it is
then this X.gro file (guanidium + thiocynate ion + water ) will be input
for -cs flag in genbox for particular concentration in different size of
box?



Kinshuk Raj Srivastava
IIT-Bombay
India