[gmx-users] gromacs rerun calculate the energy
348363213 at qq.com
Mon Jul 31 14:04:15 CEST 2017
I used Gromacs run the biological system, which contains water, ions(Na+,Cl-), and nucleic. I used gromacs run the system, and the coulombtype was PME and the cutoff was 10 angstrom, then I want to use the commond rerun to calculate the interaction of resid 1 and resid 2, I add the energygrps in my mdp, and the coulombtype was PME, the .edr file can be obtained. Then I use g_energy to calculate the coulomb interaction. I have three question.
first, when the rcoulomb=10 angstrom, and coulombtype=PME, within 10 angstrom, is PME algorithm using ?
second, The PME algorithm dived into long range interaction and short range interaction, whereas we only calculate the short range of the coulomb energy using Gromacs, can we obtain the long range of the coulomb energy?
Third, when I use rerun to calculate the coulomb energy, the rcoulomb from 1.0 nanometre change to half of the water box I built, and the coulombtype from PME to cut-off, is it reasonable to calculate the coulomb energy?
thank you very much.
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