[gmx-users] Thermodynamic integration and re-weighting method

[Alex]

Hi Gozde,

I also use something similar, by an simple pull restrain(distance) to keep
a counter ion close to the charged molecule which is under perturbation in
FEP.
These type of restrains are \*Lambda  *independent and if I am not wrong
their portion in free energy change should be calculated analytically by a
formula like something you will see in below link in its "removal of
restrains" section;

http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme

But I have not been able to use it applicably, and I would be also
appreciated if you could let me also know how to use if you find out either
by this or ... .

Best regards,

Alex

On Mon, Oct 17, 2016 at 6:14 PM, gozde ergin <gozdeeergin at gmail.com> wrote:

> Any idea?
> Thanks.
> > On 13 Oct 2016, at 15:42, gozde ergin <gozdeeergin at gmail.com> wrote:
> >
> > Dear all,
> >
> > I will use Gromacs to calculate the chemical potential difference of
> solvation a surfactant molecule on the surface.
> > System covers water molecules covered with surfactant molecules.
> > I will apply flat-bottom restraint to the surfactant molecules in order
> to stabilise them on surface. I will not let them to go inside the bulk.
> > My question is how should I re-weight the free energy value to remove
> the effect of flat-bottom restraint potential?
> >
> > Thanks in advance.
>
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