[gmx-users] free energy decomposition
David van der Spoel
spoel at xray.bmc.uu.se
Wed Oct 13 20:42:41 CEST 2010
On 10/13/10 8:30 PM, Chris Neale wrote:
> This is not possible using g_energy or any other gromacs tool that I am aware of.
> You must calculate the temperature derivative of the free energy.
> See, for example, equation 16 in Pettitt BM, Rossky PJ. J Chem Phys. 1986;84:5836
Recent versions of gromacs will actually plot the enthalpy in the energy
file, and since your are only interested in the enthalpy difference that
would work *if it wasn't for the umbrella sampling*. I think if you had
used constraints rather than umbrellas this might do the trick.
Temperature dependence is of course a dependable way as well.
> -- original message --
> I am studying Potential of mean force(PMF) of association of two peptides. I
> want to decompose the PMF into energy(enthalpy) and entropic terms. But, I have
> some queries on how to extract those contributions .
> I found, in literature, generally, people try to get the energy(enthalpy)
> first and then subtract it from PMF to get the entropic contribution. My
> question is related to how to get the energy term first:
> 1. Will it be appropriate to just use g_energy tool on ener.edr file for each
> windows obtained from umbrella sampling and select the 'potential energy'
> functionality term to get the*average potential energy* for each windows ?
> I used energy groups = system in the .mdp file for each windows of my umbrella
> sampling simulations.
> 2. If it is so, now I wonder whether g_energy will give that potental energy
> *in presence of umbrella bias* . If it is true, do one need to first unbias the
> energy some how ( like using a boltzman factor) ? However, I do not how to do
> if you provide any ideas, that will be great .
> Here is the details on what I have done to get the PMF .
> I am studying Potential of mean force(PMF) of association of two peptides. For
> this purpose , I have carried out GROMACS 4.0.7 umbrella sampling simulation by
> dividing the reaction coordinate( i.e distance between center of mass of two
> peptides) into around 25 windows of 0.1 nm separation. Now, I have used WHAM
> and got the PMF by unbiasing the umbrella potential.
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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