[gmx-users] Testing gromacs: Thermodynamics integration using tabulated potential

[Fahimeh Baftizadeh]

Dear Mark,

Thanks for your reply.
Before this test, I have performed several thermodynamics integration
playing with the number of lambda points and also decoupling first coulomb
and then VDW or decoupling both at the same time. All my tests gave the
same results as long as I am not using tabulated form of potential. In all
of them, I obtained 74kj/mol as solvation free energy!

Now, my question is that, why using tabulated potential makes that much of
a difference?
Do you mean that decoupling both Q and VDW can be a problem while using
tabulated potential? In any case, I will lunch a simulation decoupling them
separately and will update you.

I really appreciate your help
Fahimeh


On Tue, May 27, 2014 at 1:06 PM, Fahimeh Baftizadeh <
fahimeh.baftizadeh at googlemail.com> wrote:

> Dear Mark,
>
> Thanks for your reply.
> Before this test, I have performed several thermodynamics integration
> playing with the number of lambda points and also decoupling first coulomb
> and then VDW or decoupling both at the same time. All my tests gave the
> same results as long as I am not using tabulated form of potential. In all
> of them, I obtained 74kj/mol as solvation free energy!
>
> Now, my question is that, why using tabulated potential makes that much of
> a difference?
> Do you mean that decoupling both Q and VDW can be a problem while using
> tabulated potential? In any case, I will lunch a simulation decoupling them
> separately and will update you.
>
> I really appreciate your help
> Fahimeh
>
>
>
> On Tue, May 27, 2014 at 12:20 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
>
>> Hi,
>>
>> Decoupling both q and vdw at the same time is not a good idea. You should
>> observe that at nearly-disappeared lambda, the error bars grow
>> dramatically.
>>
>> Mark
>>
>>
>> On Tue, May 27, 2014 at 5:38 PM, Fahimeh
>> <fahimeh.baftizadeh at googlemail.com>wrote:
>>
>> > Hi everyone,
>> >
>> > I am computing solvation free energy of molecule A in solvent B. I used
>> > two different procedure and I thought that the results should be
>> > comparable, however they are very different.
>> >
>> > Procedure 1:
>> > Thermodynamics integration using 20 lambda points. VDWtype was switch
>> and
>> > I used PME coulombtype.  I turned off VDW and coulomb interactions both
>> at
>> > the same time. The free energy of solvation was  74kj/mol
>> >
>> > Procedure 2:
>> > Thermodynamics integration using 20 lambda points. I introduce tabulated
>> > potential for the interaction between molecule A and molecule B.
>> therefore
>> > the vdwtype and columbtype was set to User. I provided two files, called
>> > table.xvg and table_A_B.xvg which are identical for now as a test. These
>> > files contain, r, 1/r, 1/r**2, -1/r**6, -6/r**7, 1/r**12, 12/r**13.  The
>> > other parameters for VDW interactions are untouched. The result of this
>> > simulation however is very different ~ 50kj/mol ...
>> >
>> > I am expecting to receive not identical but something comparable ...
>> could
>> > you please help me to understand this?
>> >
>> > Many thanks in advance
>> >
>> > Fahimeh
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> ---------------------------------------------------------------------------------------------------
> "If you torture the data long enough, they will confess to anything!" John
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