On 6/12/12 10:09 AM, [email protected] wrote:
On 6/12/12 8:48 AM, [email protected] wrote:
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.
But when I want only the water atoms to be minimized and to run the md
simulation only for the water atoms I have to restrain the whole protein
or not? I already googled around a lot and I found many many examples
for
.mdp files.
Is it possible to run an md simulation with the following .mpd file?
Sure, it's possible, but perhaps you can clarify a few things, because
there are
a number of inconsistencies in what you've been saying.
1. EM and MD are different processes. If you want to minimize the
position of
only H atoms and keep others restrained, use the .mdp file I provided
above. I
doubt it will accomplish much though, since you're restraining a large
part of
the system.
2. I though you were working in vacuo? Where do you have explicit water?
Is
this some sort of droplet simulation? If it is, then using the infinite
cutoff
approach is probably not appropriate. There are a number of posts about
such
topics in the list archive and there is published literature in very good
journals about how to do such simulations.
The .mdp file below will be very inaccurate. Using a plain cutoff for
Coulombic
interactions is not appropriate with a finite value for rcoulomb. The
.mdp file
will also cause the program to run forever (with nsteps = -1), unless you
kill
it or something else does. You're also producing no output at all to a
trajectory, energy file, or log file, so there's not much use in running
MD
forever just to get nothing. If you're trying to accomplish EM, then
using the
"md" integrator is incorrect, you need an EM algorithm.
I want to do two different things.
First I wanted to minimize the hydrogens of the protein, leave the rest of
the protein fix and do this in vacuum.
This already worked. Thank you!!
But now the next step is to run a md simulation with this minimized
structure. And again I only want to do the simulation for the hydrogens of
the protein and again in vacuum.
OK, then take note of everything I said before, because your .mdp is not set up
to do this, and there are certain settings that will certainly lead to an
unstable trajectory. If you want to simulate in vacuum, don't set implicit
solvent parameters. Use infinite cutoffs (rlist=rcoulomb=rvdw=0) and set a
fixed number of steps.
Note that your simulation probably won't do much. If the heavy atoms are
position-restrained, and the H atoms constrained to them (since you've set
all-bonds for constraints), then nothing is likely to move very much at all.
Remember to set non-zero values of nst* if you want actual output.
-Justin
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = -1
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = cut-off
vdwtype = cut-off
rcoulomb = 1.0
rvdw = 1.0
pbc = no
epsilon_rf = 0
rgbradii = 1.0
comm_mode = angular
implicit_solvent = GBSA
gb_algorithm = HCT
gb_epsilon_solvent = 78.3
sa_surface_tension = 2.25936
nstxout = 0
nstfout = 0
nstvout = 0
nstxtcout = 0
nstlog = 0
nstcalcenergy = -1
nstenergy = 0
tcoupl = berendsen
tc-grps = system
tau-t = 0.1
ref-t = 300
Eva
-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
--
========================================
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
--
========================================
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
