[gmx-users] LIE with a 20 A water shell

David van der Spoel spoel at xray.bmc.uu.se
Thu Oct 6 08:52:04 CEST 2005


On Wed, 2005-10-05 at 17:03 -0500, tivi wrote:
> Dear Gromacs users,
> 
> I want to calculate the free energy of binding between a ligand and its 
> receptor. First I would like to try the linear interaction energy 
> method.
> 
> Throughout the literature, a 20 A radius water shell is used to solvate 
> both the ligand and the complex (i.e., ligand-receptor).
> Any idea how to do this using gmx?
We haven't implemented a potential for restraining atoms within a
sphere.


> Regards,
> Tivadar Orban
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++





More information about the gromacs.org_gmx-users mailing list