[gmx-users] Umbrella sampling - decomposing of free energy

David van der Spoel spoel at xray.bmc.uu.se
Fri Jul 17 18:07:40 CEST 2015

On 17/07/15 17:54, gozde ergin wrote:
> Dear gromacs users,
> I did umbrella sampling in order to estimate the PMF profile of my system.
> My system has 512 water molecules covered by 25 decanol molecules on both
> side.
> I pulled a water molecule bulk water to organic layer and than gas phase.
> (Please see the system pic , http://imgur.com/sFFlVjF )
> As a next step I wanted decompose this free energy in enthalpic and
> entropic contribution
> Delta G = Delta H - T Delta S
> Enthalpies ΔH were computed by averaging the potential energy over the
> respective simulation trajectory in each window (see the pic
> http://imgur.com/tc3cO95 )
> My question is as you see there is big variation in enthalpy.
> What should I do to get more precise (less varied) potential energy?
> Simulation time 4 ns, time step is 2 fs, force field os GAFF (produced by
> topolbuild)
> As an example here one of the window potential energy
> http://imgur.com/Bw9aUpu
> Thanks in advance
Unfortunately the energy needs roughly ten times longer to equilibrate 
than the PMF!

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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