[gmx-users] Coul-SR energy component - CG simulation

[Carlos Navarro Retamal]

Dear gromacs users,
I’m studying the interaction between protein and several mixture lipids (POPC-MGDG, POPC-DGDG, POPC-SQDG).
All simulations ran successfully.
Analysing the energy componentes during the simulations i noticed that when i calculated the Coul-SR energy componen Between the protein and each thylakoid membrane i got this:

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Coul-SR:Protein-DGDG              0          0          0          0  (kJ/mol)

And that doesn’t have any sense. Looking into the simulation i noticed how the protein and membranes are interacting, so i don’t know what may be happening (the LJ-SR term showed a more favorable interaction with respect to the thylakoid lipid membrane rather than to the POPC membrane).
Is this normal? I’m really worried about these.
By the way, i’m using a shift potential to describe coulomb and vdw interactions (since martini force field was parametriced in that way),do you think that maybe this issue is because i’m not using PME to describe this interaction?
Best,
Carlos


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Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl