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. 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?
what other insights do you guys have to the differences? thank you very
much. i'll also present the em.mdp i used below:
title = em
cpp = /lib/cpp
define = -DFLEXIBLE
constraints = none
integrator = cg
dt = 0.002
nsteps = 100000
nstlist = 10
ns_type = grid
rlist = 0.8 ;short range
rcoulomb = 1.4 ;long range
rvdw = 1.4 ;long range
;
; Energy minimizing stuff
;
emtol = 1
emstep = 0.001
nstcgsteep = 10
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