[gmx-users] simulating ligands attached to a surface...?

T.A.Wassenaar T.A.Wassenaar at rug.nl
Thu Apr 21 21:04:46 CEST 2005

Hi Daniel,

What you want is well possible. In the topology file for 
the ligand (ligand.itp) add a something like:

[ position_restraint ]
    1    1000    0    0

Here, the first number is an atom identifier, 
corresponding to an atom under [ atoms ] and the number 
are the force constants for the restraints in the x, y and 
z direction. The directions in which it should move freely 
should be set to 0, obviously. Also check the manual (in 
case i misspelled something).

Hope it helps,


On 21 Apr 2005 17:37:37 +0000
  Daniel Rigden <drigden at liverpool.ac.uk> wrote:
> Hi all
> Can anyone tell me if it's straightforward, or even 
>possible to simulate
> ligands that are attached to a surface?  The ligands are 
> attached but may 'skate' around the two-dimensional 
>surface.  I was
> imagining that the atoms through which the ligands are 
>attached could be
> constrained in z while being free to explore x and y. 
> All the other
> atoms would explore x, y and z as normal.  Is that 
>possible in Gromacs?
> Thanks very much for any advice
> 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
> Crown St.,
> Liverpool L69 7ZB, U.K.
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