[gmx-users] Spherical constraint (spherical force)

Jochen Hub jochen at xray.bmc.uu.se
Mon Oct 17 15:36:42 CEST 2011

Hi Mikhail,

we hard-coded the flat-bottom potential into bondfree.c which is in 
src/gmxlib. I send you the source file in a separate e-mail.

The patch will replace all position restraints by a flatt-bottom 
spherical potential with a flat radius of 1.4nm. If you want a different 
radius you'll have to change the bondfree.c, look for the posre 
function. It's a quite dirty inflexible hack, but it was good enough for 
us. So you cannot have normal position restraints and the flat-bottom 
restraints at the same time.

Note that you must define the reference position of all the position 
restraint potentials with the -r option of grompp. E.g., if your droplet 
is at the origin, you need a gro/pdb file with all coordinates set to 
0,0,0 to be used with the -r option. The position restraints are defined 
as usual in the [ position_restraints ] sections in the topology.

I hope this helps, please let us know if something is unclear.


On 10/17/11 Oct 17,2:41 PM, Mikhail Stukan wrote:
> Dear gmx-user,
> I would like to simulate an isolated  drop of water (without PBC). To  
> prevent water molecules form evaporation I would like to create a 
> spherical constraint around the system. In recent article in PNAS 
> (Caleman, Hub, van Maaren, van der Spoel,  v. 108, 6838 (2011)) where 
> the authors considered similar system it is mentioned that:
> "To avoid such evaporation, we applied a spherical flat-bottom 
> quadratic potential acting on the water. That potential was 
> implemented as an additional force F pointing toward the COM of the 
> droplet..."
> Could anybody give a hint how this approach can be realized in 
> GROMACS? I looked through the manual, but did  not find clear answer 
> how to implement such a force.
> Thank you very much in advance.
> Mikhail
> =============================================
> Dr Mikhail Stukan
> Schlumberger Dhahran Carbonate Research Center,
> Dhahran Techno Valley  - KFUPM,
> P.O. Box 39011, Dammam / Doha Camp  31942,
> Kingdom of Saudi Arabia
> Tel: +966 3 331 6182
> Fax:+966 3 330 0845
> mstukan at slb.com <mailto:mstukan at slb.com>

Dr. Jochen Hub
Computational and Systems Biology
Dept. of Cell&  Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4715056 Fax: +46-18-511755

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