[gmx-users] calculating free energy

Felipe Merino felipe.merino at mpi-dortmund.mpg.de
Sun Apr 19 11:39:08 CEST 2015


In principle, you can do umbrella sampling with the number of native 
contacts as your collective variable. I remember that this was possible 
with the first PLUMED and I assume it can be arranged for the new 
version. If this converges or not is of course a whole different story. 
I assume that a mixture with some sort of hamiltonian exchange would be 

However, even if possible I'd be extremely cautious with the end result 
since there is a lot of force field bias in this things. The fact that 
they can reproduce which one is the lowest energy conformation (which is 
already awesome) does not mean that they can say by how much.


On 04/19/2015 03:41 AM, Christopher Neale wrote:
> 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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Felipe Merino, Dr. rer. nat.
Max Planck Institute for Molecular Physiology
Department of Structural Biochemistry
Otto-Hahn-Str. 11
44227 Dortmund
Phone: +49 231 133 2306

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