On 6/12/12 7:46 AM, [email protected] wrote:
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.
okey, thanks a lot!!
But when I want to do a whole md run after this minimization my first .mdp
file was correct, right?
For running in implicit solvent, that .mdp file has a number of problems.
By restraining the protein, you don't really accomplish anything. Also note
that for using implicit solvent, you generally need infinite cutoffs (like in
the case of the "vacuum" .mdp file I posted before) and no pressure coupling. I
have found that with finite cutoffs, energy conservation is poor and structures
are unstable when using implicit solvent.
There are a number of useful discussions in the list archive about such
considerations; I would encourage you to spend some time reading before diving
headfirst into something that may not turn out well.
-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
