Re: size of water box and cellbasisvectors

From: Ajasja Ljubetič (
Date: Wed Mar 30 2016 - 08:08:14 CDT


I usually put 5-10 Angstrem spacing on each side.
And then I get the cell basis vector using min/max (sometimes adding a 0.5
A just to be on the safe side).


### center the protein and also measure the min/max

set allp [atomselect top "all"]

measure center $allp

measure minmax $allp

set dims [measure minmax $allp]; vecsub [lindex $dims 1] [lindex $dims 0]

# center the protein

$allp moveby [vecinvert [measure center $allp]]
$allp delete

On 30 March 2016 at 14:51, faride badalkhani <>

> Dear all,
> Could you give me some information how to determine the size of water box
> in
> package require solvate
> solvate system.psf system.pdb -t X -o system_wb
> command.
> And, what is the best way to determine cellbasisvectores? Is that
> reasonable to use minmax command and then use the maximum coordinate?
> Truly yours,
> Farideh

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