[gmx-users] a question on energygrps

[Justin Lemkul]

On 7/14/13 6:21 AM, Albert wrote:
> Hello:
>
>   I've got a question on energygrps options in .mdp file. This option is usually
> used for  establishing the groups for the energy output. I am going to study the
> entropy changes of protein-ligand-SOL in a membrane system, I am just wondering
> shall I specify each compoenent in energygrps option, like:
>
> energygrps          =  Protein LIG SOL POPC
>

This setting will give you pairwise-decomposed nonbonded energies between these 
groups, but it has nothing to do with entropy.

> I am also going to use g_lie for interaction analysis, will the above options be
> sufficient?
>

No.  The LIE method requires a separate simulation of the ligand in water to 
acquire ligand-water interaction energies.  In the case of a heterogeneous 
system like yours (including a membrane), I don't know that the LIE assumptions 
hold since you don't necessarily have simple partitioning between aqueous and 
protein-bound states.

> If I forgot to assign the energygrps options in my md.mdp file during MD
> simulations, is it any fast way to calculate the energy after MD instead of
> running the simulation from beginning?
>

That's what mdrun -rerun is for.

> I notice that there is a tool called g_lie can be used to evaluate
> protein/ligand binding, I am just wondering is there any paper on this tool? I
> don't find too much informations on gromacs manual.
>

Nor should you - the manual is not a definitive repository of all MD-related 
knowledge :)  The literature for LIE is extensive in terms of both primary 
literature and review articles.  Apply Google or your favorite scientific database.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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