[gmx-users] surface as 'freeze group'
drigden at liverpool.ac.uk
Mon Apr 25 12:32:52 CEST 2005
Again, thanks for the quick helpful reply. Could you point me to the bit of the manual that
deals with freeze groups?
Also, does anyone have any suggestions for quick easy ways to generate the surface
that will become the freeze group? It would just be atoms regularly positioned close enough together
so as not to allow solvent to pass.
> Message: 2
> Date: Fri, 22 Apr 2005 15:40:01 +0200
> From: "T.A.Wassenaar" <T.A.Wassenaar at rug.nl>
> Subject: Re: [gmx-users] ligands bound to a surface
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <web-2883727 at mail3.rug.nl>
> Content-Type: text/plain; charset="ISO-8859-1"; format="flowed"
> Hi Daniel,
> You could do that, but indeed it's not very elegant.
> Rather, make the surface a freeze group. That way it won't
> do anything itself, except being present and keeping other
> molecules from going that way.
> On 22 Apr 2005 11:02:59 +0000
> Daniel Rigden <drigden at liverpool.ac.uk> wrote:
> > Hi again
> > Thanks, I now see that it will be possible to simulate
> >the attachment of the ligands to the surface
> > by contraining the x-coordinate (for example) of the
> >bound atom. However, there's another
> > potential issue I just thought of.
> > The ends of the ligands are away from the surface,
> >exposed to solvent. The system would
> > therefore be put in a solvent box. But the solvent
> >should not be allowed to reappear at the
> > surface side of the box, x=0, when it leaves the box at
> >x=box length. Is it possible to
> > turn off this behavious selectively for one face of the
> >box? Or what I have to include an
> > explicit surface to prevent this happening? Could I
> >simply place a 2D array of atoms at
> > x=0 and fix their positions using big position_restraint
> >values? That doesn't seem very elegant.
> > Thanks again for your help
> > Daniel
Dr Daniel John Rigden Tel:(+44) 151 795 4467
School of Biological Sciences FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool
Liverpool L69 7ZB, U.K.
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