[gmx-developers] help

[reza.khabani]

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: 

 	* Add in .mdp file "energygrps = CNT inhibitor" (in
CNT-inhibitor-Water simulation)
 	* Add in .mdp file "energygrps = inhibitor SOL" (in inhibitor-Water
simulation)
 	* 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 

 	* 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 

 	* 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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