Thanks,
Lan
On Wed, May 19, 2010 at 3:52 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Lan Hua wrote:
Hi Justin,
Thank you so much for your quick reply and good suggestions.
The following is my answer.
On Wed, May 19, 2010 at 12:50 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Lan Hua wrote:
Hi All,
I understand that the error of segmentation fault
may come
from many reasons, but I just couldn't figure out the
reason of
this error in my simulations. I want to run md
simulations with
explicit water for 20 structures of one domain (residue
77-148)
of calmodulin (PDB 1CFC). These 20 starting structures
are from
one REMD simulation in implicit water. The following is
what I
did to run simulations for these 20 structures. I used
gromacs
version 3.1.4 with ffamber ports. The force field is amber03
and water model is TIP3P.
Do you have any particular reason for using software that is
eight
years old? You will get a massive performance upgrade with
4.0.7, as
well as the ability to use multiple processors per replica. In
versions prior to 4.0, you can only use one processor per
REMD replica.
The reason that I am using gromacs 3.1.4 is to prepare some
input files for simulations at fold...@home in which version
3.1.4 is recommended.
OK, as long as you've got a reason...
1. get rid of the steric clash in the starting structure
What do you mean? Energy minimization? How did you did do this
prior to step 2 (generating a topology)?
I used the "protein preparation wizard" which is implemented in
maestro package to do this. Actually in this wizard, energy
minimization is performed on protein.
2. after doing pdb2gmx, then minimze the protein
3, use "-bt dodecahedron -d 0.9 -c" in the command
line of
editconf
4, after doing genbox, first minimize the water with
protein
rigid and then minimize the whole system
A lot of these steps are redundant and probably unnecessary.
Some tips:
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
Thanks for the tips. I went to the link, but I am still a little
bit confused about which steps are unnecessary. You mean step 7
and step 8? I did this in case simulations at f...@h would be crashed.
I just mean the repeated, separate energy minimizations. I guess
there's no harm in it, but generally I find that minimizing the
protein in vacuo, then with and without restraints in solvent, etc.
is unnecessary. I'd suggest just building the system (solvent and
all), and minimizing the whole thing (without restraints). I don't
think you stand to gain anything with your procedure.
5, run md simulation with position restraint for protein
heavy atoms with nose-hoover thermostat for 20ps
6, run NPT simulations with nose-hoover thermostat and
Parrinello-Rahman thermostat for 500ps
7, run NVT simulation for another 100ps
8, then energy minimze the whole system again.
Every time, there are always "segmentation fault" in step
6 for
some starting structures which could be different in
every try.
I checked the energy, volume, pressure, temperature, etc for
the trajectories which are crashed because of segmentation
fault, but nothing was wrong. I roughly checked the
trajectory
which looks fine. I also couldn't find any useful
information
from the log file, which looks like the following:
Using weak coupling (i.e. Berendsen) coupling is generally
recommended for initial equilibration. If a system is far from
equilibrium (as it likely will be after adding patterned
blocks of
water with genbox), the N-H thermostat can allow for wild
changes in
the temperature of the system, leading to a collapse.
Your temperature coupling groups are also inappropriate:
Tcoupl = nose-hoover
tc_grps = Protein SOL Na
tau_t = 0.1 0.1 0.1
Never couple solvent and ions separately; it can lead to
instability:
http://www.gromacs.org/Documentation/Terminology/Thermostats
These are good suggestions. Thanks. So use Berendsen coupling
for both temperature and pressure coupling for initial
equilibration, for example position restrained NVT followed by
NPT, right? I have another
At least for the thermostat, but yes, probably it can't hurt to use
weak coupling for both temperature and pressure.
question. If I choose constraints = hbonds instead of
constraints = all-bonds in NPT simulation, what will happen?
You constrain heavy atom-H bonds instead of all bonds. Using fewer
constraints may or may not affect the magnitude of the time step you
can use, but generally X-H bonds are the highest frequency and thus
are the least stable with long time steps.
-Justin
Best,
Lan
-Justin
Step Time Lambda Annealing
180000 360.00003 0.00000 1.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.045887 47 48 0.004584
After LINCS 0.000020 752 755 0.000003
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell.
LJ-14 Coulomb-14
2.08335e+03 1.59908e+02 2.95659e+03
1.17109e+03 1.27711e+04
LJ (SR) Disper. corr. Coulomb (SR) Coulomb
(LR) Potential
4.10779e+04 -1.37728e+03 -2.89916e+05
-5.82443e+04 -2.89318e+05
Kinetic En. Total Energy Temperature Pressure (bar)
5.25584e+04 -2.36759e+05 2.96920e+02 -1.07683e+02
Step Time Lambda Annealing
185000 370.00003 0.00000 1.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.052014 70 71 0.005149
After LINCS 0.000011 214 215 0.000002
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell.
LJ-14 Coulomb-14
2.33684e+03 1.42695e+02 2.91169e+03
1.18452e+03 1.28507e+04
LJ (SR) Disper. corr. Coulomb (SR) Coulomb
(LR) Potential
4.06987e+04 -1.37332e+03 -2.88889e+05
-5.83180e+04 -2.88455e+05
Kinetic En. Total Energy Temperature
The *.mdp files are also attached. Any help will be highly
appreciated. Thank you.
Best,
Lan
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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