[gmx-users] calculating free energy

Christopher Neale chris.neale at alum.utoronto.ca
Sun Apr 19 03:41:21 CEST 2015

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.


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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