[gmx-users] Simulation in Vacuum

[xieyh at hkusua.hku.hk]

Dear GMX users:

I'd like to simulate a protein in vacuum, but the mdrun run has always been
crashed. I think my *.mdp file is not correct. Can anybody give it a
correctness?

em.mdp:
////////////////////////
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
dt                  =  0.002
nsteps              =  500
;
;	Energy minimizing stuff
;
emtol               =  2000
emstep              =  0.001

nstcomm             =  1
ns_type             =  grid
rlist               =  1.0
coulombtype         =  PME
rcoulomb            =  1.0
rvdw                =  1.2
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no
////////////////////////////////

pr.mdp:

title               =  Yo
cpp                 =  /lib/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002	
nsteps              =  5000	
nstcomm             =  1
nstxout             =  50
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
coulombtype         =  PME
rcoulomb            =  1.0
rvdw                =  1.4
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 two groups
Tcoupl              =  berendsen
tc-grps		  =  protein
tau_t               =  0.1    
ref_t               =  300    
energygrps	  =  system;
;Pressure coupling is off
Pcoupl              =  no
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529
///////////////////////////////////////

full.mdp:

title               =  Yo    
cpp                 =  /lib/cpp    
constraints         =  all-bonds    
integrator          =  md
dt                  =  0.002	
nsteps              =  200000	
nstcomm             =  1
nstxout             =  1000
nstvout             =  10000
nstfout             =  1000
nstlog              =  1000
nstenergy           =  1000
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
coulombtype         =  PME
rcoulomb            =  1.0
rvdw                =  1.4
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 two groups
Tcoupl              =  berendsen
tc-grps             =  protein
tau_t               =  0.1       
ref_t               =  300     
; Energy monitoring
energygrps          =  system
; Isotropic pressure coupling is now on
Pcoupl              =  no
; Generate velocites is off at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529



Thanks and regards,
Xie YH