yes this is how you generate an initial structure, which needs multi-step
equilibration.
is there reason to think that something has not worked properly?
On Wed, May 19, 2010 at 2:05 PM, John S <s.john634.gmail.com> wrote:
> Dear All,
>
> While creating a solvent box I followed the following steps :
> x= loadpdb tem.pdb
> alignaxes x
> set x box 10
> set x restype solvent
> desc x
>
> UNIT name: Molecule
> Head atom: null
> Tail atom: null
> Periodic box: 10.00000, 10.00000, 10.00000
> Contents:
> R<SUBUNIT 1>
>
> solute =loadpdb ccl.pdb
> solvatebox solute x 10
>
> Solute vdw bounding box: 42.058 199.760 29.041
> Total bounding box for atom centers: 62.058 219.760 49.041
> Solvent unit box: 10.000 10.000 10.000
> Total vdw box size: 47.193 218.991 43.896 angstroms.
> Volume: 453655.599 A^3
> Total mass 63122.844 amu, Density 0.231 g/cc
> Added 410 residues.
>
> Here my question is that though it solvates my solute , the solvent box is
> not equilibrated .
>
> If I go for solvatebox solvent solvent 10
>
> The solvent molecule is at center surrounded my other solvent
> molecules.Will
> it be the proper initial structure for the equilibration steps .
>
> Please suggest .
>
> Thanks
> John.
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Received on Wed May 19 2010 - 13:30:03 PDT
