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>> 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> | (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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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