[gmx-users] forcefield and setting

[fatemeh ramezani]

 Dear Justin
I used gromacs OPLSAA forcefield for simulation of protein and TIP3P model for water.

em.mdp file:
title               =  n.pdb
cpp                 =  /lib/cpp
define              =  -DFLEXIBLE
constraints         =  none
integrator          =  steep
nsteps              =  40000
constraint_algorithm  =
shake_tol           = 0.0001
nstenergy           =  10
nstxtcout           =  1
nstlist             =  5
nstcomm             =  1
ns_type             =  grid
rlist               =  1
coulombtype         =  PME
rcoulomb            =  1
rvdw                =  1
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  8
ewald_rtol          =  1e-5
optimize_fft        =  yes
emtol               =  1000.0
emstep              =  0.01

md.mdp file:
title               =  n.pdb restraining
cpp                 =  /lib/cpp
constraints         =  none
integrator          =  md 
dt                  =  0.0008
nsteps              =  25000000
nstcomm             =  10
comm_mode           =  
nstxout             =  250
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  0.9
coulombtype         =  PME
rcoulomb            =  0.9
rcoulomb-switch     =  1
rvdw                =  0.5
vdwtype             =  shift
;rvdw-switch         =  0.6
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  6
ewald_rtol          =  1e-5
optimize_fft        =  yes
  

; Berendsen temperature coupling is on in three groups
Tcoupl              =  V-rescale
tau_t               =  0.1       0.1
tc-grps            =  Protein   Non-Protein
ref_t               =  300       300
; Pressure coupling is  on
;Pcoupl              =  berendsen
Pcoupl              =  no
Pcoupltype         =  isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529
energygrps          = Protein  Sol 



Fatemeh Ramezani