[gmx-users] Fwd: Dodecahedron Box size and Appropriate number of SOL molecules

[Apramita Chand]

Dear Experts,
 I am trying to simulate a peptide in urea-water mixture in GROMOS53a6 ff.
Since rvdW=1.4 in this case, any box length less than ~2.8 gives errors
like
ERROR 1 [file topol.top, line 133]:
  ERROR: The cut-off length is longer than half the shortest box vector or
  longer than the smallest box diagonal element. Increase the box size or
  decrease rvdw.
 Hence I've to choose a box size of 2.9angstroms and above.
I'm trying to ascertain the number of water molecules that are needed to
solvate the system.
Say I've to solvate a box of my peptide and 5 urea molecules...I can't just
go ahead with whatever number of solvent molecules I have in mind,can
I?-maxsol and -nmol options wouldn't give the optimum number of water
molecules actually needed to solvate the box.
So,is the number of SOL molecules which are added by genbox completely
acceptable? Is it calculated on the basis of volume or something else? Any
particular rules or formulae as to how many molecules can fit inside the
rhombic dodecahedron ?

I would also like some advice on what precautions are to be taken or any
special changes in parameters that need to be done when handling
dodecahedron boxes.


Regards,
Apramita Chand