[gmx-users] mdrun seems stuck

[Stefano Meliga]

Hello,

I'd like to run a position restrained MD of a protein in water with
3000 (protein) + 40000 (SOL) atoms.

I preprocess the input with the command line:

$grxdir/grompp -f 4AKEprePRMD.mdp -po 4AKE_PRMD.mdp -c 4AKE_EMcg.gro
-p 4AKEallHion.top -pp 4AKEprePRMD.top -o 4AKE_PRMD.tpr

4AKEprePRMD.mdp is:

title               =  4AKE_PRMD
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  5000     ; total 10.0 ps.
nstcomm             =  1        ; [steps] frequency for center of mass
motion removal
nstxout             =  100      ; [steps] frequency to write
coordinates to output trajectory file
nstvout             =  100      ; [steps] frequency to write
velocities to output trajectory
nstfout             =  0        ; [steps] frequency to write forces to
output trajectory
nstlog              =  10       ; [steps] frequency to write energies
to log file
nstenergy           =  10       ; [steps] frequency to write energies
to energy file
nstlist             =  5        ; neighbour searching
ns_type             =  grid
rlist               =  1.0
coulombtype         =  EWALD
rcoulomb            =  1.0
vdwtype             =  Cut-off
rvdw                =  1.0

; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tau_t               =  0.1              0.1
tc-grps             =  Protein          Non-Protein
ref_t               =  300              300
; Energy monitoring
energygrps          =  Protein          SOL
; Pressure coupling is on
Pcoupl              =  berendsen
Pcoupltype          =  isotropic
tau_p               =  0.5
compressibility     =  4.5e-5   ; [1/bar] compressibility of water
ref_p               =  1.0      ; [bar] reference pressure for coupling
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529


Then I run the PR MD:
$grxdir/mdrun -s 4AKE_PRMD.tpr -o 4AKE_PRMD.trr -c 4AKE_PRMD.gro -e
4AKE_PRMD.edr -g 4AKE_PRMD.log -v

These lines appear on the terminal:
starting mdrun 'Protein in water'
5000 steps,     10.0 ps.

...but from this point on nothing more is displayed. I see neither
steps nor time left.
Are the parameter in the mdp file defining a too expensive simulation?

I've tryied removing pressure and temperature coupling but the problem remains.
How can I solve this issue?

-DPOSRES refers to posre.itp, I guess. posre.itp was created from the
original pdb before the energy minimization. Should I run pdb2gmx once
again after the EM to create a new posre.itp?

Thanks,

Stefano