[gmx-users] SR and LJ energies

[Michal Kolinski]

Thank you for comment.  I really don't know where the problem might be.  
I also got very small coulomb SR energies for 1ns MD of similar system.
Maybe there is some problem with my *.mdp file.  
Thanks for help.   

    

MICHAL


title               =  morph_opioid_rec_lipid_w_i
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  hbonds
integrator          =  md
dt                  =  0.002 ; 
nsteps              =  1000000  ; 
nstxout             =  10000
nstvout             =  10000
nstfout             =  10000
nstlog              =  1000
nstenergy           =  1000
nstxtcout           =  1000
nstlist             =  10
ns_type             =  grid
rlist               =  1.0

; Method for doing VdW
vdw-type            =  Cut-off
rvdw                =  1.0

; Method for doing electrostatics
coulombtype         =  PME
rcoulomb            =  1
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  4
ewald_rtol          =  1e-5
optimize_fft        =  yes




; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps      =  DPPC Protein DRG   SOL Cl
tau_t               =  0.1   0.1   0.1  0.1 0.1
ref_t               =  300    300   300   300 300
; Energy monitoring
energygrps          =  DPPC  Protein DRG SOL Cl 
; Isotropic pressure coupling is now on

;-----------------------nowe----------------
Pcoupl              =  berendsen
Pcoupltype          = semiisotropic
tau_p               =  10   10   
compressibility     =  0    4.5e-5
ref_p               =  1.0  1.0




; Generate velocites is off at 300 K.
;gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529
;freezegrps          =  C-alpha 
;freezedim           =  Y Y Y   
; Groups for center of mass motion removal
comm-grps            =  DPPC  Protein DRG SOL Cl
; Mode for center of mass motion removal
comm-mode            =  Linear
; Center of mass control
nstcomm              =  1

; Periodic boundary conditions
pbc                  =  xyz
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