[gmx-developers] problem in calculation of linear interaction energy

Erik Lindahl erik.lindahl at gmail.com
Thu Jan 6 18:18:44 CET 2022

Hi Reza,

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On Thu, Jan 6, 2022 at 5:58 PM reza.khabani <reza.khabani at ut.ac.ir> wrote:

> Dear Developer of Gromacs,
> I want to calculate energy binding with the LIE method in Gromacs, but
> Gromacs 2021 cannot read the energy file correctly (ener.edr). For this
> purpose, I will explain the simulation step by step so that if there is a
> problem, help me solve this problem. CNT and inhibitor molecules are
> simulated in water. An additional simulation (Inhibitor in water) is
> required to calculate energy binding with the LIE method. According to the
> Gromacs Manual, I went through all the steps as follows:
>    1. Add in .mdp file "energygrps = CNT inhibitor" (in
>    CNT-inhibitor-Water simulation)
>    2. Add in .mdp file "energygrps = inhibitor SOL" (in inhibitor-Water
>    simulation)
>    3. The following commands were executed to simulate the
>    inhibitor-Water:
> gmx grompp -f binding_energy2.mdp -c run.gro -p topol.top -o binding.tpr
> -maxwarn 13
> gmx mdrun -s binding.tpr -rerun run.xtc –nb cpu –deffnm ener2
> gmx energy -f ener2.edr -o bindingenergy.xvg -b 9000 > binding.log
> Select the inhibitor-SOL option
> Elj=29.338 ,Eqq=-419.446
>    1. The following commands were executed to simulate the
>    CNT-inhibitor-Water:
> gmx grompp -f binding_energy1.mdp -c run.gro -p topol.top -o binding.tpr
> -maxwarn 13
> gmx mdrun -s binding.tpr -rerun run.xtc –nb cpu –deffnm ener
>    1. The “gmx lie” command was used to calculate energy binding in the
>    last step.
> gmx lie -f ener.edr -b 9000 -Elj 29.338 -Eqq -419.446 -ligand inhibitor -o
> lie.xvg
> At this point, *Gromacs cannot extract the relevant data from the
> ener.edr file and the numbers it reports are unrealistic and incorrect*.
> Thank you for helping me solve this problem.
> I wish you all the best,
> Reza Khiabani
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Erik Lindahl <erik.lindahl at dbb.su.se>
Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm
Science for Life Laboratory, Box 1031, 17121 Solna, Sweden

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