[gmx-users] Implicit solvent - Gromacs 4.5.4

[Vedat Durmaz]

hi steven,

i've been simulating a 33 AA peptide for the past two days using 
implicent solvent in order to achieve a proper folding.

i haven't added counterions, however, the systems shows nice results 
according to what i've expected. the mdrun command (for the extension) 
for our hardware looks as follows:

mpiexec -np 4 mdrun -pd -s md.tpr -append -cpi md.cpt -deffnm md 2>&1

and here's the mdp file for the energy minimization:

define              =  -DFLEXIBLE
constraints         =  none
integrator          =  steep
dt                  =  0.001    ; ps
nsteps              =  30000
vdwtype             =  cut-off
coulombtype         =  cut-off
pbc                 =  no
nstlist             =  0
ns_type             =  simple
rlist               =  0       ; this means all-vs-all (no cut-off), 
which gets expensive for bigger systems
rcoulomb            =  0
rvdw                =  0
comm-mode           =  angular
comm-grps           =  Protein
optimize_fft        =  yes
;
;       Energy minimizing stuff
;
emtol               =  5.0
emstep              =  0.01
;
; Implicit solvent
;
implicit_solvent    =  GBSA
gb_algorithm        =  Still ; HCT ; OBC
nstgbradii          =  1
rgbradii            =  0   ; [nm] Cut-off for the calculation of the 
Born radii. Currently must be equal to rlist
gb_epsilon_solvent  =  80    ; Dielectric constant for the implicit solvent
; gb_saltconc       =  0     ; Salt concentration for implicit solvent 
models, currently not used
sa_algorithm        =  Ace-approximation
sa_surface_tension  = -1


and for the md run:

define              =  -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES
constraints         =  none
integrator          =  md
dt                  =  0.001   ; ps
nsteps              =  1000000000 ; 100000 ps = 100 ns
nstcomm             =  10
nstcalcenergy       =  10
nstxout             =  1000     ; frequency to write coordinates to 
output trajectory
nstvout             =  0       ; frequency to write velocities to output 
trajectory; the last velocities are always written
nstfout             =  0       ; frequency to write forces to output 
trajectory
nstlog              =  1000         ; frequency to write energies to log 
file
nstenergy           =  1000     ; frequency to write energies to edr file

vdwtype             =  cut-off
coulombtype         =  cut-off

pbc                 =  no

nstlist             =  0
ns_type             =  simple
rlist               =  0       ; this means all-vs-all (no cut-off), 
which gets expensive for bigger systems
rcoulomb            =  0
rvdw                =  0

comm-mode           =  angular
comm-grps           =  system

optimize_fft        =  yes

; V-rescale temperature coupling is on
Tcoupl              =  v-rescale
tau_t               =  0.1
tc_grps             =  system
ref_t               =  300
; Pressure coupling is off
Pcoupl              =  no
; Generate velocites is on
gen_vel             =  yes
gen_temp            =  300
gen_seed            =  -1

;
; Implicit solvent
;
implicit_solvent    =  GBSA
gb_algorithm        =  Still ; HCT ; OBC
nstgbradii          =  1
rgbradii            =  0   ; [nm] Cut-off for the calculation of the 
Born radii. Currently must be equal to rlist
gb_epsilon_solvent  =  80    ; Dielectric constant for the implicit solvent
; gb_saltconc       =  0     ; Salt concentration for implicit solvent 
models, currently not used
sa_algorithm        =  Ace-approximation
sa_surface_tension  = -1


best regards,
vedat


Am 28.02.2012 11:59, schrieb Steven Neumann:
> Dear Gmx Users,
> I am using Gromacs 4.5.4 and I would like to implement implicit 
> solvent for folding of my protein. I read mailing list and it is still 
> confusing for me.
> Is it proper to use counterions within the system? If not, how can I 
> obtain netral system?
> Do we use cut off for vdw and coulombic interactions?
> What kind of integrator should be used with a timestep?
> I will appreciate an mdp file for protein folding! Thank you
> Steven