[gmx-users] Ewald setting for hydrocarbon system?
joojoojooon at gmail.com
Fri Jul 9 17:26:27 CEST 2010
I need your favor. I have a hydrocarbon system with no charged particles.
Today In one of the GROMACS tutorials I saw the following setting in em.mdp
fourierspacing = 0.12
;fourier_nx = 0
;fourier_ny = 0
;fourier_nz = 0
;pme_order = 4
;ewald_rtol = 1e-5
;optimize_fft = yes
has been used for PME . Sofar I did not even include coulombtype=PME in my
em.mdp file. What I had was:
constraints = all-bonds
integrator = steep
dt = 0.002 ; ps !
nsteps = 200
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
; Energy minimizing stuff
emtol = 1000.0
Can you please guide me whether it is necessary to include these lines in em
file for system having only partial charges like hydrocarbon (alkane). Also,
in md.mdp file I have only coulombtype=PME and not the above Ewald settings.
Do you recommend to include those settings? Without the mentioned lines I am
getting reasonabel results (potential energy, kinetic, ,, also T coupling
works perfectly). If I had better to unclude them what is the best value for
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