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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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