[gmx-users] simulating ligands attached to a surface...?
T.A.Wassenaar at rug.nl
Thu Apr 21 21:04:46 CEST 2005
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
> Dr Daniel John Rigden Tel:(+44) 151
> School of Biological Sciences FAX:(+44) 151
> Room 101, Biosciences Building
> University of Liverpool
> Crown St.,
> Liverpool L69 7ZB, U.K.
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