both oct or cubic should be fine, especially for your simple system, as long as they are equilibriated later.
--- 11年10月8日，周六, Yun Shi <yunshi09.gmail.com> 写道：
发件人: Yun Shi <yunshi09.gmail.com>
主题: [AMBER] oct or cubic box?
收件人: "AMBER Mailing List" <amber.ambermd.org>
日期: 2011年10月8日,周六,上午2:15
Hi all,
I am solvating my protein with TIP3P water with ambertool1.5.
I found that when using
solvatebox aba TIP3PBOX 12.0
I got
Solute vdw bounding box: 77.859 58.790 54.861
Total bounding box for atom centers: 101.859 82.790 78.861
Solvent unit box: 18.774 18.774 18.774
Total vdw box size: 104.734 85.784 81.867 angstroms.
Volume: 735533.609 A^3
Total mass 369758.800 amu, Density 0.835 g/cc
Added 17853 residues.
while using
solvateOct aba TIP3PBOX 12.0
I got
Scaling up box by a factor of 1.300525 to meet diagonal cut criterion
Solute vdw bounding box: 81.041 46.469 55.176
Total bounding box for atom centers: 112.254 112.254 112.254
(box expansion for 'iso' is 87.8%)
Solvent unit box: 18.774 18.774 18.774
Volume: 726322.374 A^3 (oct)
Total mass 401178.704 amu, Density 0.917 g/cc
Added 19597 residues.
So what does the "scaling up" or "expansion" mean when using octahedral box?
Between this two solvation strategies, is it better to use the latter one
since the density is more close to 1g/cc ?
Thanks for any help!
Yun Shi
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Received on Sun Oct 09 2011 - 17:30:02 PDT
