Thanks All.
I saved the file as pdb and prmtop and inpcrd files of the solvent.
For the equilibration steps ,I am running MD
- constant volume for 200 picosecs heating to 300K and then
-equilibrating at 300K at constant pressure run till I get the experimental
density of chlorobenzene.
Can you explain how should I do a multistep equilibration or how should I go
about in the equilibration steps .
Thanks
John.
On Wed, May 19, 2010 at 4:11 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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 Thu May 20 2010 - 20:30:03 PDT
