> First, number of ions is determined from the water box volume. For
> example, 113 NaCl ions gives me 0.3M salt concentration based on the
> water box volume, which is generated from "solvatebox mol TIP3PBOX 12.0
> 0.832".
You likely do not want to add the water after the ions as you point out
since the box is too big. The problem with initial placement you had
post-solvation is a LEaP bug that has yet to be tracked down. The work
around that I've found is to add the ions a few at a time or 1 at a time.
One at a time always works. Although this takes longer, in principle it
is a better means to place ions since the approximate electrostatic
potential is re-calculated each time the command is called. In general,
however, I simply randomize the ion placement with ptraj after ion
placement with "randomizeions" anyways...
aa = loadpdb model.pdb
solvateoct aa TIP3PBOX 14.0 iso
addions aa Na+ 0
addions aa Na+ 1 Cl- 1
addions aa Na+ 1 Cl- 1
addions aa Na+ 1 Cl- 1
addions aa Na+ 1 Cl- 1
addions aa Na+ 1 Cl- 1
addions aa Na+ 1 Cl- 1
addions aa Na+ 1 Cl- 1
addions aa Na+ 1 Cl- 1
addions aa Na+ 1 Cl- 1
addions aa Na+ 1 Cl- 1
--tec3
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Received on Thu Feb 02 2012 - 16:00:02 PST
