[gmx-users] Re: script to remove water (Kai Zhuang)

John Simms jxs818 at bham.ac.uk
Wed Aug 24 17:50:48 CEST 2005

An alternative is to (temporarily) increase the size of the carbon atom in
the $gromacs/share/top/vdwradii.dat file from 0.15 to say 0.45 and then use
genbox to hydrate your box. Once it is done just change the carbon value
back to what it was. You will see a zone between the water and the lipids
but this can be rectified by having a positional restraint on the lipids and
allowing the water to rest (20ps or so).

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