[gmx-users] calculating free energy

[nazli kashani javid]

thanks for your anwers.


On Tue, Apr 21, 2015 at 7:10 AM, lloyd riggs <lloyd.riggs at gmx.ch> wrote:

>
> In general a realistic unfolded system would have to start at several
> random points in state A, and allowing it to fold into state B.  This
> accounts for gaussian distributions of random states...
>
> these tend to be long as the folding process is between 200 (for short) to
> 5-6 usecounds for longer proteins...
>
> Some tricks...
>
> 1) starting from a half folded state, however this will not give your
> entire energy system from A to B
> 2) setting up the system with a chaperone protein (structures are in the
> PDB)...this gives a more rapid, but biological vs. in solvent state...
> 3) Reducing your system size, as unfolded proteins take up more volumn in
> a unit cell, thus every 20-40 nanoseconds, stop, reduce the unit cell
> volumn, then continue, which allows the larger scale simulations to be
> achieved much faster
>
> The bar method works great for smaller molecules, but not proteins, as it
> if you read the paper is based on constants derived from a few hundred real
> kinetic determined states for small molecules.  These are not a linear
> curve for proteins, and are usually protein specific, or even larger
> molecule specific if you go higher than 100 atoms...
>
> Dont know what your doing though...
>
> Sincerely,
>
> Stephan L. Watkins, PhD
>  *Gesendet:* Sonntag, 19. April 2015 um 03:41 Uhr
> *Von:* "Christopher Neale" <chris.neale at alum.utoronto.ca>
> *An:* "gromacs.org_gmx-users at maillist.sys.kth.se" <
> gromacs.org_gmx-users at maillist.sys.kth.se>, "gmx-users at gromacs.org" <
> gmx-users at gromacs.org>
> *Betreff:* Re: [gmx-users] calculating free energy
> How about temperature replica exchange with de novo folding, then convert
> the probabilities of the folded and unfolded states into a free energy
> difference? You'll obviously need to be really careful about cutting off a
> sufficient amount of initial simulation time as equilibration, but you
> might be able to get a good idea of how much to cut if you repeated it once
> from unfolded and once from folded.
>
> Chris.
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of nazli
> kashani javid <nazlikjavid at gmail.com>
> Sent: 18 April 2015 11:24
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] calculating free energy
>
> Hi all,
>
> I know there are some methods for calculating free energy of* binding*
> between a ligand and a receptor.
>
> 1.Are there any methods for calculating free energy of *unfolding
> *proteins?
>
> 4_helix bundle protein makes my system,
>
> 2.Is scientifically reasonable for my system to calculate free energy in
> the same way as described in tutorial number 6, methane in water ( coupling
> parameter : vdw interaction)?
>
> Thank you
>
> any help is appreciated.
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