[gmx-users] Umbrella sampling - decomposing of free energy
gozdeeergin at gmail.com
Fri Jul 17 18:12:22 CEST 2015
On Fri, Jul 17, 2015 at 6:07 PM, David van der Spoel <spoel at xray.bmc.uu.se>
> 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
>> 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
>> As an example here one of the window potential energy
>> 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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