Linear Interaction Energy

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1

GROMACS version: 2023.1
GROMACS modification: No
Here post your question

I have simulated sorption of two compounds on a surface. After running LIE, I get the following values:
Compound 1: DGbind = 651.570
Compound 2: DGbind = 574.912 (-nan)

I have a question here: Does the lower DGbind of compound 2 means it is binding moe strongly?

Thanks,
Raman

2

Dear Gromacs Community,

I believe my previous post was not sufficiently explanatory so I am posting with more info.

I ran MD of sorption of a few molecules on a surface. The molecules were simulated in 1) water and 2) sorbed on a surface in water. CHARMM36 FF was used with TIP3P water. After calculating LJ and Coulombic energies from system 1), I used those with gmx lie to get interaction energy.

My questions are:

  1. I believe that LIE represents energy of transfer from water to the surface. Is this correct?
  2. A lower energy value indicates that the binding is preferred for that compound (as is usually the case with dG)? LIE values in my case are >500. Is this value expected for a long polymer chain?

Thanks in advance for help.

Regards,
Raman