On Wed, Feb 20, 2008, abiram abiram wrote:
>
> 1) Can somebody tell me which of the line in the above gives the
> dimension of the box.
The "total vdw box size". To double-check, look at the last line of the crd
file you made.
>
> 2) I want to know, whether that dimension is considered as the unit
> cell boxlengths for PBC simulations.
Yes.
>
> 3) Also why there is a large difference in the thrid parameter of
> the lines indicating "Solute vdw bounding box, Total bounding box
> for atom centers, Solvent unit box, Total vdw box size ".
The "solute" is probably not very spherical, as it appears to be about 10 Ang.
longer in the x and y directions than in the z direction. After waters are
added to a certain distance around the solute, the same difference is present.
Using a visualization program to examine your files may help here.
...dac
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Feb 24 2008 - 06:07:08 PST
