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

[Justin A. Lemkul]

Anirban Ghosh wrote:
> 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-moltype
> 
> 

The name of the moleculetype you want to decouple.  Presumably your ligand.

>         couple-lambda0
> 
> 

...and couple-lambda1, right?  These settings will depend on which part of the 
nonbonded interactions (van der Waals and Coulombic interactions) you're 
decoupling.  Check out the free energy tutorial linked on the Gromacs site for 
the underlying theory of what to do, even if the settings have changed somewhat. 
  The type of interaction you're decoupling will also dictate whether or not you 
should use soft-core.

>         couple-intramol
> 

If you're looking for an absolute binding energy, then set this to "no."

-Justin

> 
>         Thanks a lot again.
> 
> 
> 
> Regards,
> 
> Anirban
> 
> On Sat, Nov 27, 2010 at 9:15 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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-- 
========================================

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

========================================