On 10/12/12 9:39 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
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?
Your time step (5 fs) is much too high unless you are using virtual sites.
Reduce it to 2 fs.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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