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

[gozde ergin]

But why?

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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