I'd imagine that most of those numbers are historical and were chosen to
produce "reasonable" system sizes compared to the cutoff by assuming the
experimental bulk density. Although, many of them may not have even been
produced with AMBER programs. For example, I believe the magical 216 number
for TIP3P is from the original Monte Carlo simulations by Jorgenson
(although I have no idea if AMBER uses the* same* box, just the number).
In any event, the solvatexxx commands in Leap stack multiple copies of
those boxes together and then pare away molecules to reach the desired
buffer size and cell shape (maybe someone else can explain how this
actually happens). You can usually see this if you immediately visualize
the structure, as there are often gaps where the box "seams" are matched
together so as to avoid steric clashes. This also results in water boxes,
for example, being about 15% lower density than the actual model predicts
(~0.7 vs ~0.9 or so for TIP3P).
Regards,
Brian
On Thu, Sep 26, 2013 at 12:53 PM, Chinthaka Ratnaweera <cnr88.msstate.edu>wrote:
> Hi
>
> I have rather general question about solvent boxes used in amber.
> I noted that different solvent boxes have different number of residues per
> box. For example TIP3PBOX has 216, MEOHBOX has 125, and CHCL3BOX has 1375
> residues per box. How does this determined? Is it just arbitrarily
> selected? If I am making a new solvent box, is there a optimal number of
> residues to be taken?
>
> Thank you
>
> --
> Chinthaka Nadun Ratnaweera
> Hand Lab Rm 1126
> Mississippi State University
> 310 Presidents Circle
> Starkville, MS 39762
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Thu Sep 26 2013 - 11:00:03 PDT
