[gmx-users] mdp file settings for PME

jojo J joojoojooon at gmail.com
Sat Jul 10 01:54:20 CEST 2010

Dear experts,

I posted this message before but I think you did not see it since I noticed
messages after this have been replied. I have a hydrocarbon system with no
charged particles. Today In one of the GROMACS tutorials I saw the following
setting in em.mdp file:
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

Thank you,
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