Thank you David,
what you are suggesting is indeed a difference between substrate-protein
and methane-methane that seems more clearly related with the entropic
correction. If I understood well, what you mean is that the space
accessible to a ligand when it is pulled into a protein is restricted by
Chris,
I think you are correct here. For binding calculations there is
probably a further trick relating to how to define an unbound state
that has a well-defined concentration. This I think depends on how one
is pulling -- i.e. doing simple radial PMFs is probably a bad idea,
because to even conv
; > From: [EMAIL PROTECTED]
> > To: gmx-users@gromacs.org
> > Subject: [gmx-users] Entropy correction in PMF
> >
> > That sentence could definitely use some massaging. Try this:
> >
> > Whether one needs to correct for this contribution depends on what
> the
> Date: Wed, 23 Apr 2008 20:34:40 -0400
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Entropy correction in PMF
>
> That sentence could definitely use some massaging. Try this:
>
> Whether one needs to correct for this contribution d
That sentence could definitely use some massaging. Try this:
Whether one needs to correct for this contribution depends on what the
pmf should represent. When one wants to pull a substrate into a protein,
this entropic term indeed contributes to the work to get the substrate
into the protein. Thi
I sent the attached message on last March 31 but I didn't get any
answer... may be the right people was not available at that time and
that is why I am trying again. I would thank a lot to have some more
detail about this paragraph in the gromacs manual (version 3.3, chapter
6, page 111):
“Whether
Dear all,
My question is related to the calculation of absolute binding Gibbs energies
more than to the use of Gromacs but it is motivated by a paragraph of the
Gromacs manual version 3.3 (and also on several papers by Gilson, Karplus,
and others), so I hope someone can help me.
We have cal
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