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.
Jochen
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
[email protected] <mailto:[email protected]>
--
---------------------------------------------------
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
http://xray.bmc.uu.se/~jochen/index.html
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