[gmx-users] g_lie useage

[Justin Lemkul]

On 11/4/13 1:52 AM, Saman Shahriyari wrote:
> dear gmx users
> i am trying to use g_lie tool regarding the fact i am a
>   newbie to this. so i searched through the web for an appropriate
> protocol. although there are lots of staffs discussing the theory, but i
>   couldn't find any thing describing the steps techniqally and with some
> details.
> generally speaking, this is what seemed to me as the steps
> that i need to go through (it would be the kind of you to help me know
> if they are correct and what is missing):
> 1-runnig two md simulations for free and bond ligand (using PME)
> 2-
>   doing the mdrun with -rerun flag by using the new .mdp (as is prepared
> in gmx forum:
> http://gromacs.5086.x6.nabble.com/Doubts-over-g-lie-usage-td5000130.html)
>   and the old .tpr file.

Do not use the old .tpr file.  If you make changes to the .mdp file, then they 
will not take effect unless you re-run grompp and use the new .tpr file.

-Justin

> 3- using g-energy to extract Elj and Eqq from ligand simulation in water (using the outputs of step 2 )
> 4- using the g-lie command by introducing Elj and Eqq  to it, in order  to have the final free energies of binding.
> i do appreciate your kind help
> saman
>

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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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