[gmx-users] how to introduce vacuum??

[Bert de Groot]

Oliver Beckstein wrote:
> 
> On Tue, 5 Aug 2003, Pedro Alexandre Lapido Loureiro wrote:
> 
> > > 1: i have one water box with a protein & some other molecules. the
> > >height ( 'c' in the dimensions of the system) of the box is 60
> > >angstroms. Now I have to introduce vacuum in a section of the box (
> > >say from height of 45 AU to 55 AU) how do i do that??
> 

[..]

> I admit that this script is a bit too complicated (after all, a simple awk
> would (almost) do the job, too) but it worked for me sofar *provided there
> are less than 100,000 atoms* in your gro file---otherwise strange things
> happen (any hints & feedback appreciated).
> 


this small awk might do the job too (on a pdb file):

($3 != "HW1" && $3 != "HW2") {keep[$5]=1}
($3 == "OW" && ($8 > 45 && $8 < 55)) {keep[$5]=0}
keep[$5]==1 {print $0}


(provided that the pdb does *not* contain chain identifiers, otherwise
the $8 should be a $9 and the $5 a $6).

--

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________