[gmx-users] Umbrella Sampling Hypericin Dimer

[Justin A. Lemkul]

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

-- 
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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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