On 6/12/12 7:34 AM, [email protected] wrote:
On 6/12/12 7:05 AM, [email protected] wrote:
On 6/12/12 5:54 AM, [email protected] wrote:
Hi everybody,
I tried to run a minimization just of the hydrogen of a membrane
protein.
I want to do this in vacuum.
But when I started the run with
mpirun mdrun_mpi -deffnm protein -v -nt 2
I get the error that there is a segmentation fault.
Threading and MPI parallelization are independent. You can't use both.
If
you've compiled with MPI support, you can't invoke the -nt option.
okey, I'll try it without the -nt option. But I still get the error
But when I only type
mpirun mdrun_mpi
there is no problem so I guess that my already produced input files
are
the problem. For example I am not completely sure about the .mdp file.
Can
you please give me an example for a .mdp file for a minimization of
only
the hydrogen but not the whole protein in a vacuum.
It would be far more useful for you to post what you're using so we can
provide
The .mpd file I use looks like this:
define = -DPOSRES
integrator = md
tinit = 0
dt = 0.005
nsteps = 20000
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 1000
nstxtcout = 1000
nstenergy = 1000
energygrps = Protein Non-Protein
nstcalcenergy = 5
nstlist = 5
ns-type = Grid
pbc = xyz
rlist = 0.9
coulombtype = Cut-off
rcoulomb = 0.9
rvdw = 0.9
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 298 298
Pcoupltype = Isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = no
constraints = all-bonds
constraint-algorithm = Lincs
unconstrained-start = yes
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
implicit_solvent = GBSA
gb_algorithm = HCT
nstgbradii = 1.0
rgbradii = 0.9
gb_epsilon_solvent = 80
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
Your goal is energy minimization of H atoms in a vacuum, correct? Your
.mdp
file is for a full MD simulation using an NVT ensemble in implicit
solvent.
What you want is something more along the lines of:
define = -DPOSRES
integrator = steep
emtol = 1000.0
emstep = 0.01
nsteps = 50000
energygrps = system
nstlist = 1
ns_type = simple
rlist = 0
coulombtype = cutoff
rcoulomb = 0
rvdw = 0
pbc = no
but how does the minimization "know" that it should be in vacuum.
There's nothing particularly special about running in vacuum except that there
is no solvent. Infinite cutoffs and a nonperiodic simulation cell are common
conventions for simulating in vacuum, so that's what the .mdp file above does.
-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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
