On 4/30/12 12:26 PM, Hovakim Grabski wrote:
Dear Gromacs users,
I want to set up an umbrella sampling simulation of an Hypericin dimer.
I have created position restraint filesfor hypericin with genrestr and then
use it with the topology file, so I want to know if it is just restraining one
of the Hypericin Molecules or both of them?
That depends on how your topology is set up. Position restraints are applied
per moleculetype, so if you have defined one moleculetype for this molecule and
simply specified two of those molecules in the .top, it is applied globally.
If the two molecules are restrained , how can I restrain just one of the
Hypericin molecules?
In this case you would need two distinct [moleculetype] directives in the
topology, though they would be identical. Only one of them would specify a
[position_restraints] directive.
For running umbrella sampling of two molecules in water, there is no need for
position restraints at all. The only biasing potential you need is the one
maintaining a distance between the two molecules.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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