[gmx-users] Umbrella sampling - decomposing of free energy
David van der Spoel
spoel at xray.bmc.uu.se
Sat Jul 18 09:16:56 CEST 2015
On 17/07/15 18:11, gozde ergin wrote:
> But why?
Larger fluctuations I guess.
People find this in other packages too so it is a physical phenomenon.
> 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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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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