[gmx-users] question about NVT run

[reisingere at rostlab.informatik.tu-muenchen.de]

Hi everybody,
I want to do a md run for my membrane protein. For this I first did the
energy minimization run.
This finished with no errors. Here is the output of it:

Steepest Descents did not converge to Fmax < 10 in 5001 steps.
Potential Energy  = -8.7463000e+05
Maximum force     =  4.5984982e+02 on atom 1107
Norm of force     =  5.0847759e+00


The mdp file contains:

define                  = -DPOSRES
integrator              = steep
emtol                   = 10
nsteps                  = 5000
nstenergy               = 1
energygrps              = System
coulombtype             = PME
rcoulomb                = 0.9
rvdw                    = 0.9
rlist                   = 0.9
fourierspacing          = 0.12
pme_order               = 4
ewald_rtol              = 1e-5
pbc                     = xyz



Now I want to do a NVT to run to prepare the MD run. But here I get the
error:

Segmentation fault
mdrun -nice 0 -c protein.pdb -compact -deffnm protein -s protein.tpr -v
2>> nvtLogErr >> nvtLogOut


And there are is no protein.pdb file as output but only step.pdb files
like step43b_n6.pdb

The mdp file looks like this:

define               = -DPOSRES
integrator           = md
dt                   = 0.005
nsteps               = 10000
nstxout              = 0
nstvout              = 0
nstfout              = 0
nstlog               = 1000
nstxtcout            = 0
nstenergy            = 5
energygrps           = Protein Non-Protein
nstcalcenergy        = 5
nstlist              = 10
ns-type              = Grid
pbc                  = xyz
rlist                = 0.9
coulombtype          = PME
rcoulomb             = 0.9
rvdw                 = 0.9
fourierspacing       = 0.12
pme_order            = 4
ewald_rtol           = 1e-5
gen_vel              = yes
gen_temp             = 200.0
gen_seed             = 9999
constraints          = all-bonds
tcoupl               = V-rescale
tc-grps              = Protein  Non-Protein
tau_t                = 0.1      0.1
ref_t                = 298      298
pcoupl               = no


I already did this but the last time I fixed all atoms except of the
hydrogen atoms because I wanted to do a MD run with them and keep the rest
of the  structure.
But know I want to do the MD run with all the side chains. And now the
error occurs.

Can you please tell me what a segmentation fault means? Is this because of
the mdp file or because of the protein?

Thank you,
Eva