rob yang wrote:
hi list,
i am comparing the relative energy differences between different
conformations of a same molecule in vaccuum. i am using both gromacs and
another software to compare the results. the forcefield for both
softwares is oplsaa (2001), and i've manually verified that they are
indeed the same for my molecule as well as the partial charges.
the relative energy results obtained from these 2 softwares are
different. i understand that different softwares have different
implementations but i think i should be able to get a similiar relative
energies for these conformations.
so i am thinking maybe the minimizations is where things went wrong.
Have you looked at the resulting structures to see if you are comparing
the same states? Watching the minimization "trajectories" will help you
assess what differences there may be. Ordinarily I would pick a
structure minimized with one program and then just do an energy
calculation on the other, if I wanted to do this sort of calculation.
It's quite similar to what quantum chemists do all the time - get
geometries at one "level of theory" and then calculate energies at
another more expensive one whose cost is prohibitive for optimization.
i
have compiled the double version of mdrun. but i didn't for grompp since
i didn't think it was necessary. the question i have for you guys is
then: is the double version of grompp also necessary?
I doubt single/double mdrun will matter to you for geometry
optimization. I don't know if double grompp is necessary to make double
mdrun effective - my guess would be not necessary.
what other insights do you guys have to the differences? thank you very
much. i'll also present the em.mdp i used below:
It looks unremarkable.
Mark
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