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

[Tsjerk Wassenaar]

Hi Apramita,

First of all, your box diameter should be the length of the peptide plus 2,
with a minimum of 2.8. Otherwise, the peptide will be able to interact
directly with its periodic image.

The solvent is typically added by overlaying a box of pre-equilibrated
solvent and deleting all molecules that are outside the target box or
overlap with those present in the target box. If you want control over the
amount of water added, the easiest way is to take a box size which gives a
bit more water than you need, and delete a number of molecules. The
equilibration steps will make things right for you.

There are no precautions or problems with rhombic dodecahedron boxes.
They're the best for many purposes.

Cheers,

Tsjerk


On Tue, Jun 7, 2016 at 8:20 AM, Apramita Chand <apramita.chand at gmail.com>
wrote:

> 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
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-- 
Tsjerk A. Wassenaar, Ph.D.