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

[gozde ergin]

Thank you very much for your responds. I will run longer simulations.

On Sat, Jul 18, 2015 at 9:17 AM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> 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>
>> wrote:
>>
>>  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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>>
>
> --
> 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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