[gmx-users] Free Energy Calculation: dVpot/dlambda is always zero

[Anirban Ghosh]

Hello Justin,

Thanks a lot for the reply.
Yes, I am using GROAMCS 4.5 and my system consists of two chains of two
proteins, a substrate and an inhibitor solvated in water. So can you please
tell me what should be the values for:
couple-moltypecouple-lambda0couple-intramolThanks a lot again.


Regards,

Anirban

On Sat, Nov 27, 2010 at 9:15 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Anirban Ghosh wrote:
>
>>
>> Hi ALL,
>>
>> I am trying to run free energy calculation and for that in the md.mdp file
>> I am keeping the following option:
>>
>> ; Free energy control stuff
>> free_energy     = yes
>> init_lambda     = 0.0
>> delta_lambda    = 0
>> sc_alpha        =0.5
>> sc-power        =1.0
>> sc-sigma        = 0.3
>>
>>
>> But still I find that in my log file the values for dVpot/dlambda is
>> always coming to be zero.
>> What I am doing wrong?
>> Any suggestion is welcome. Thanks a lot in advance.
>>
>>
> You haven't indicated your Gromacs version, but assuming you're using
> something in the 4.x series, you're not specifying the necessary parameters
> to do any sort of transformation, particularly couple_lambda0 and
> couple_lambda1.  If left at their default values (vdw-q), nothing gets
> decoupled.
>
> -Justin
>
>
>> Regards,
>>
>> Anirban
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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