> In xleap I did the following:
>
> solvatebox x TIP3PBOX 5
> Solute vdw bounding box: 34.786 34.000 24.736
> Total bounding box for atom centers: 44.786 44.000 34.736
> Solvent unit box: 18.774 18.774 18.774
>
> Total vdw box size: 47.686 47.275 37.638 angstroms.
> Volume: 84849.507 A^3
> Total mass 30854.016 amu, Density 0.604 g/cc
> Added 1046 residues.
>
> In mdin the cut off is 10 A
The standard approach is to always have your md cutoff be ~2A less
than your box clearance. So typically
solvatebox x TIP3PBOX 10
with cutoff of 8A
Or more expensively,
solvatebox x TIP3PBOX 12
with cutoff of 10A
This ensures that after the box shrinks to a density of 1 g/cc, no
water will interact with solute in more than one direction. E.g.
|___5A___solute___5A___|...5A...[solute]...5A...|
where '|' is a box wall. With cutoff of 10, each water will 'see'
both images of the solute. This introduces unwanted correlation.
Bill
>
>
> Thanks
> Kirtana
>
> On Wed, Dec 7, 2011 at 6:19 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > > My simulation run has good enengetics for a high solute concentration
> > about
> > > (by wt%) and also goes through ,whereas when I use this fo a 50wt% of
> > > solute concentration I get severe temperature
> > > rise
> >
> > What leap solvatebox cutoff did you use, and what cutoff in mdin?
> >
> > Bill
> >
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Received on Wed Dec 07 2011 - 18:00:02 PST
