**From:** Oleksii Zdorevskyi (*zdorevskyi_at_bitp.kiev.ua*)

**Date:** Fri Oct 14 2022 - 04:59:58 CDT

**Next message:**Ankita Kandalkar: "Error: Constraint failure in RATTLE algorithm for atom 5298"**Previous message:**Brian Radak: "Re: When should I use NTER and NNEU as a patch?"**Next in thread:**Marcelo C. R. Melo: "Re: how to properly calculate the interaction between the QM and MM region"**Reply:**Marcelo C. R. Melo: "Re: how to properly calculate the interaction between the QM and MM region"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dear NAMD community,

I have a question regarding the calculation of interaction energies in

QM/MM simulations. I have browsed through previous NAMD-l discussions,

however, did not find any similar topics.

According to the NAMD QM/MM paper (Melo, Marcelo CR, et al. "NAMD goes

quantum: an integrative suite for hybrid simulations." Nature methods 15.5

(2018): 351-354.), the total *potential* energy of the system is computed

in the following way:

E(total) = E(MM) + E(QM) + E(QM/MM),

where E(MM) is the energy of the classical part, E(QM) - is the

single-point energy calculated by the QC software, and E(QM/MM) is the

interaction energy between the classical and quantum regions.

Now, I need to plot these 3 components as separate time series.

When I browse through the log file, I can see the "QMENERGY" keyword,

which corresponds to the E(QM) (actually, I checked it by comparing this

value with the corresponding single-point energy from ORCA output).

Then, I can extract the energy called "POTENTIAL" from the same log file.

If I understand correctly, this energy contains all the interactions in

the system, including van der Waals between the classical and quantum

part, as well as Coulomb interaction between classical charges, and

single-point charges derived from the previous QM step (when we use

"electrostatic embedding"). Does this energy describe E(tot), listed in

the formula above, correct?

If I subtract the "QMENERGY" (E(QM)) from the "POTENTIAL" (E(tot)), it

will give me the following:

E(MM)+E(QM/MM),

so E(MM) and E(QM/MM) can be only obtained as a sum.

However, I need to plot separate contributions for E(MM), E(QM), and

E(QM/MM).

Are there any means to extract them from NAMD output?

I will appreciate your help.

Best regards,

Oleksii

**Next message:**Ankita Kandalkar: "Error: Constraint failure in RATTLE algorithm for atom 5298"**Previous message:**Brian Radak: "Re: When should I use NTER and NNEU as a patch?"**Next in thread:**Marcelo C. R. Melo: "Re: how to properly calculate the interaction between the QM and MM region"**Reply:**Marcelo C. R. Melo: "Re: how to properly calculate the interaction between the QM and MM region"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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