AMBER Archive (2007)

Subject: AMBER: Solvent in closest contact with solute

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat Sep 01 2007 - 09:15:11 CDT

In the analysis of qmmm procedures (Amber9) for a 98-atoms non polymeric
molecule in explicit methanol or chloroform boxes, I would like to examine
(VMD) the solute with its closest lying solvent residues, all other solvent
residues being removed. Which is the best ptraj option to this regard?

A related, perhaps even more naive question: which relationship, if any,
between the physical solubility of the solute and the number of solvent units
in the box? In the perspective of periodicity. At the limit: any meaning in
carrying out simulations in an explicit solvent where the physical solubility
of the given solute barely attains the value for UV spectra (while the molar
absorbance is quite sizable).

Thanks
francesco pietra

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