[gmx-users] vacuum simulations

[tasneem kausar]

Dear gromacs users

I have performed the vacuum simulation of protein.
The structure was minimized after generating the box using the following
mdp parameters.
;
;    User spoel (236)
;    Wed Nov  3 17:12:44 1993
;    Input file
;
cpp                 =  /usr/bin/cpp
define              =  -DFLEX_SPC
constraints         =  hbonds
integrator          = steep
nsteps              =  3000
;
;    Energy minimizing stuff
;
emtol               =  2000
emstep              =  0.01

nstcomm             =  1
ns_type             =  simple
rlist               =  0.0
coulombtype         =  cut-off
rcoulomb            =  0.0
rvdw                =  0.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
Tcoupl              =  no
Pcoupl              =  no
PBC                 =  no
gen_vel             =  no


then i have run the full md for 5ns.
mdp parameter are as follows:

;
;    User spoel (236)
;    Wed Nov  3 17:12:44 1993
;    Input file
;
title               =  Yo
cpp                 =  /usr/bin/cpp
constraints         =  hbonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  2500000    ; total 5000 ps.
nstcomm             =  1
nstxout             =  500000
nstvout             =  500000
comm-mode           =  ANGULAR
lincs_iter          =  2
nstfout             =  0
nstlog              =  500
nstenergy           =  500
nstxtcout           =  500
xtc-precision       =  1000
nstlist             =  10
ns_type             =  simple
rlist               =  0.0
coulombtype         =  cut-off
rcoulomb            =  0.0
rvdw                =  0.0
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              =  no
tc-grps            =  Protein
tau_t               =  0.1
ref_t               =  300
; Energy monitoring
energygrps          =  Protein
; Isotropic pressure coupling is now on
Pcoupl              =  no
Pcoupltype          = isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529
PBC                 =  no


Is this a right way to perform the MD in vacuum?
Anyone if familiar with this procedure, please suggest.


Thanks in Advance