Dear all,
I want to perform LIE calculations. I want to know what are the steps for
LIE calculations.
I know that we need to perform two simulations for Protein-Ligand and
Ligand separately.
Are these two simulations are same as we do in regular MD simulations with
EM->NVT->NPT->Prod-RUN steps?
Dear all,
I want to perform LIE calculations. I want to know what are the steps for
LIE calculations.
I know that we need to perform two simulations for Protein-Ligand and
Ligand separately.
Are these two simulations are same as we do in regular MD simulations with
EM->NVT->NPT->Prod-RUN steps?
nt: Thursday, March 16, 2017 10:29 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] LINEAR INTERACTION ENERGY
Basically you do two MD runs one with ligand in water other with ligand in
protein. You must set proper energygrps in mdp file so you get 2 edr files from
runs and in the end you use "gmx l
half of Vytautas
Rakeviius <vytautas1...@yahoo.com>
Sent: Thursday, March 16, 2017 10:29 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] LINEAR INTERACTION ENERGY
Basically you do two MD runs one with ligand in water other with ligand in
protein. You must set proper energygrps in mdp file
Basically you do two MD runs one with ligand in water other with ligand in
protein. You must set proper energygrps in mdp file so you get 2 edr files from
runs and in the end you use "gmx lie"
(http://manual.gromacs.org/programs/gmx-lie.html) to compute difference between
those two edr
Hi gromacs users,
In order to calculate delta G (Gibbs free energy) for protein ligand binding,
what are the steps to be followed in Linear interaction energy?
Are there any tutorials for the same?
Thanks,
Kulkarni.R
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