[gmx-users] The orire_fc

[Tanping Li]

Dear David,


Thanks again for your advice. This is just a very
crude idea to restrain the water's orientation close
to protein surface. I am just curious to see, how the
rotation and translation play a role during the
solvation process respectively. I did a literature
search, but didn't see the similar work. I am even not
sure if the "orientation restrain" is possible now. Is
there something else in gromacs which can do the
similar thing?


Tanping



--- David Mobley <dmobley at gmail.com> wrote:

> Tanping,
> 
> > Thanks for your attention. I want to restrain the
> > water's orientation close to protein surface. I
> have
> > two problems:
> >
> > * what is a good reference group for the
> orientation?
> > * The orire_fc value.
> >
> > Is orientational restraints the proper function I
> > should use? Thank you again for your nice help.
> 
> I don't know and have no experience with this.
> However, in terms of
> general advice, when you ask for a specific value
> for something (i.e.
> the orientational restraints force constant) you
> probably want to
> explain what exactly you want a force constant for,
> as one would
> obviously use a very different force constant to
> restrain a water
> molecule than a protein.
> 
> Otherwise, all I can say is try and find other work
> that has
> restrained water orientations, and look to see what
> they've done and
> whether it worked well. I am not too clear on why
> you would want to do
> this.
> 
> David
> 
> >
> >
> > Tanping
> >
> >
> >
> > --- David Mobley <dmobley at gmail.com> wrote:
> >
> > > What are you trying to use orientational
> restraints
> > > to restrain?
> > > Ordinarily, you probably don't want such
> restraints,
> > > hence the default
> > > value is zero.
> > >
> > > On 7/25/06, Tanping Li <jia_11_osu at yahoo.com>
> wrote:
> > > > Hellow everyone,
> > > >
> > > > I notice that the default value for
> orire_fc=0,
> > > which
> > > > set the orientation restrain as the none. What
> is
> > > the
> > > > reasonable value for the orire_fc? Any
> suggestion
> > > will
> > > > be greatly appretiated. Thanks a lot!
> > > >
> > > >
> > > > Best
> > > > Tanping
> > > >
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